diff options
Diffstat (limited to 'metadata/md5-cache/sci-biology')
200 files changed, 2428 insertions, 0 deletions
diff --git a/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 new file mode 100644 index 000000000000..0ac48a6b6a87 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ApE-2.0.7-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=app-arch/unzip +DESCRIPTION=A Plasmid Editor +EAPI=5 +HOMEPAGE=http://www.biology.utah.edu/jorgensen/wayned/ape/ +KEYWORDS=~amd64 ~x86 +LICENSE=ApE +RDEPEND=dev-lang/tcl:0 dev-lang/tk:0 +RESTRICT=mirror +SLOT=0 +SRC_URI=http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ApE-2.0.7.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=bf78ab8abbdb34e4f7d5c8a0b4429c0f diff --git a/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 new file mode 100644 index 000000000000..a6f09e576320 --- /dev/null +++ b/metadata/md5-cache/sci-biology/GBrowse-2.48-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install postinst prepare prerm setup test unpack +DEPEND=dev-perl/Module-Build dev-perl/Capture-Tiny !<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 +DESCRIPTION=Generic Model Organism Database Project - The Generic Genome Browser +EAPI=5 +HOMEPAGE=http://gmod.org/wiki/GBrowse +IUSE=-minimal mysql postgres +sqlite vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=!<sci-biology/GBrowse-2.44-r1 >=sci-biology/bioperl-1.6.9 >=dev-perl/Bio-Graphics-2.09 >=dev-perl/GD-2.07 >=dev-perl/CGI-Session-4.02 dev-perl/IO-String dev-perl/JSON dev-perl/libwww-perl dev-perl/Statistics-Descriptive !minimal? ( dev-perl/Bio-Das >=dev-perl/Bio-SamTools-1.20 dev-perl/Crypt-SSLeay dev-perl/DB_File-Lock dev-perl/DBI mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sqlite? ( dev-perl/DBD-SQLite ) dev-perl/FCGI dev-perl/File-NFSLock dev-perl/GD-SVG dev-perl/Net-OpenID-Consumer dev-perl/Net-SMTP-SSL ) dev-lang/perl:=[-build(-)] >=app-admin/webapp-config-1.50.15 +SLOT=0 +SRC_URI=mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.48.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf webapp 6ae2395d7f341093c36057cb4f69101a +_md5_=bccaeef3292f6df307fc14fb5a2a74b2 diff --git a/metadata/md5-cache/sci-biology/HTSeq-0.9.1 b/metadata/md5-cache/sci-biology/HTSeq-0.9.1 new file mode 100644 index 000000000000..7baad9fa149a --- /dev/null +++ b/metadata/md5-cache/sci-biology/HTSeq-0.9.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] >=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files +EAPI=6 +HOMEPAGE=https://htseq.readthedocs.io/ +IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 +KEYWORDS=~amd64 +LICENSE=GPL-3+ +RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) +SLOT=0 +SRC_URI=mirror://pypi/H/HTSeq/HTSeq-0.9.1.tar.gz +_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=baebb3e5c138076f90cdaad5bc41573f diff --git a/metadata/md5-cache/sci-biology/HTSeq-9999 b/metadata/md5-cache/sci-biology/HTSeq-9999 new file mode 100644 index 000000000000..b65181b9183e --- /dev/null +++ b/metadata/md5-cache/sci-biology/HTSeq-9999 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] >=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] >=dev-vcs/git-1.8.2.1[curl] +DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files +EAPI=6 +HOMEPAGE=https://htseq.readthedocs.io/ +IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 +LICENSE=GPL-3+ +RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-biology/pysam[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) +SLOT=0 +_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 git-r3 8f6de46b0aa318aea0e8cac62ece098b multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=baebb3e5c138076f90cdaad5bc41573f diff --git a/metadata/md5-cache/sci-biology/Manifest.gz b/metadata/md5-cache/sci-biology/Manifest.gz Binary files differnew file mode 100644 index 000000000000..bf9e626eded7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/Manifest.gz diff --git a/metadata/md5-cache/sci-biology/STAR-2.5.3a b/metadata/md5-cache/sci-biology/STAR-2.5.3a new file mode 100644 index 000000000000..42bf0cc5cf13 --- /dev/null +++ b/metadata/md5-cache/sci-biology/STAR-2.5.3a @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install pretend setup +DEPEND=sci-libs/htslib:= virtual/pkgconfig +DESCRIPTION=STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays +EAPI=6 +HOMEPAGE=https://github.com/alexdobin/STAR +KEYWORDS=~amd64 +LICENSE=GPL-3 +RDEPEND=sci-libs/htslib:= +SLOT=0 +SRC_URI=https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz -> STAR-2.5.3a.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=1eb821b9192887ab1f2ac6b1536037ac diff --git a/metadata/md5-cache/sci-biology/aaindex-9.1-r1 b/metadata/md5-cache/sci-biology/aaindex-9.1-r1 new file mode 100644 index 000000000000..618805eb016b --- /dev/null +++ b/metadata/md5-cache/sci-biology/aaindex-9.1-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=Amino acid indices and similarity matrices +EAPI=6 +HOMEPAGE=https://www.genome.jp/aaindex/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/aaindex-9.1.tar.bz2 +_md5_=8636229aaffdb1c6d95611b06d3cd161 diff --git a/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 b/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 new file mode 100644 index 000000000000..a3fd873fbd89 --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-2.0.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare pretend setup +DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) misc-haskell? ( dev-lang/ghc dev-haskell/mmap ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=6 +HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ +IUSE=+mpi openmp misc-haskell +KEYWORDS=~amd64 ~x86 +LICENSE=abyss +RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) +SLOT=0 +SRC_URI=https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz -> abyss-2.0.2.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=3b173739bd4e2f9d61a49918b3b8bc05 diff --git a/metadata/md5-cache/sci-biology/abyss-2.0.3 b/metadata/md5-cache/sci-biology/abyss-2.0.3 new file mode 100644 index 000000000000..9b3eb150625c --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-2.0.3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare pretend setup +DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) misc-haskell? ( dev-lang/ghc ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=6 +HOMEPAGE=http://www.bcgsc.ca/platform/bioinfo/software/abyss/ +IUSE=+mpi openmp misc-haskell +KEYWORDS=~amd64 ~x86 +LICENSE=abyss +RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= virtual/libffi:0= ) mpi? ( sys-cluster/openmpi ) +SLOT=0 +SRC_URI=https://github.com/bcgsc/abyss/archive/2.0.3.tar.gz -> abyss-2.0.3.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=4c70cbdf60d5dc2d564272b103f2b469 diff --git a/metadata/md5-cache/sci-biology/allpathslg-52488-r2 b/metadata/md5-cache/sci-biology/allpathslg-52488-r2 new file mode 100644 index 000000000000..375f587d3cbf --- /dev/null +++ b/metadata/md5-cache/sci-biology/allpathslg-52488-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare pretend setup +DEPEND=!sci-biology/allpaths !sci-biology/vaal dev-libs/boost:= >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=De novo assembly of whole-genome shotgun microreads +EAPI=6 +HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd +KEYWORDS=~amd64 +LICENSE=MIT +RDEPEND=!sci-biology/allpaths !sci-biology/vaal +SLOT=0 +SRC_URI=ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz https://dev.gentoo.org/~mgorny/dist/allpathslg-52488-patchset.tar.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8c8bda5ab2704db1e969660ebe5882c1 diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r3 b/metadata/md5-cache/sci-biology/amap-2.2-r3 new file mode 100644 index 000000000000..9f4a18e85342 --- /dev/null +++ b/metadata/md5-cache/sci-biology/amap-2.2-r3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=java? ( >=virtual/jdk-1.5 ) java? ( >=dev-java/java-config-2.2.0-r3 ) java? ( >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 ) +DESCRIPTION=Protein multiple-alignment-based sequence annealing +EAPI=6 +HOMEPAGE=http://bio.math.berkeley.edu/amap/ +IUSE=java elibc_FreeBSD java elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=java? ( >=virtual/jre-1.5 ) java? ( >=dev-java/java-config-2.2.0-r3 ) +SLOT=0 +SRC_URI=http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-opt-2 77d2e22d0de7640f817d20e861c0ff3f java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=6bd792e8b76c06ee993b88f83e48b907 diff --git a/metadata/md5-cache/sci-biology/amos-3.1.0-r4 b/metadata/md5-cache/sci-biology/amos-3.1.0-r4 new file mode 100644 index 000000000000..fe6b48c7796e --- /dev/null +++ b/metadata/md5-cache/sci-biology/amos-3.1.0-r4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare setup +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A Modular, Open-Source whole genome assembler +EAPI=6 +HOMEPAGE=http://amos.sourceforge.net/ +IUSE=python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] dev-perl/DBI dev-perl/Statistics-Descriptive sci-biology/mummer +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=mirror://sourceforge/amos/amos-3.1.0.tar.gz https://dev.gentoo.org/~soap/distfiles/amos-3.1.0-fix-c++14.patch.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=aec6d1c76d5ea621c66e803800e2b3c4 diff --git a/metadata/md5-cache/sci-biology/arb-6.0.6 b/metadata/md5-cache/sci-biology/arb-6.0.6 new file mode 100644 index 000000000000..8fd630306977 --- /dev/null +++ b/metadata/md5-cache/sci-biology/arb-6.0.6 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare test unpack +DEPEND=app-text/sablotron media-libs/libpng:= media-libs/tiff:= www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew:= media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sys-process/time x11-misc/makedepend +DESCRIPTION=Tools for DNA/RNA sequence database handling and phylogenetic analysis +EAPI=6 +HOMEPAGE=http://www.arb-home.de/ +IUSE=debug +opengl test +KEYWORDS=~amd64 ~x86 +LICENSE=arb +RDEPEND=app-text/sablotron media-libs/libpng:= media-libs/tiff:= www-client/lynx x11-libs/libXaw x11-libs/libXpm x11-libs/motif:0 opengl? ( media-libs/glew:= media-libs/freeglut || ( media-libs/mesa[motif] ( media-libs/mesa x11-libs/libGLw ) ) ) sci-visualization/gnuplot +RESTRICT=debug? ( test ) +SLOT=0 +SRC_URI=http://download.arb-home.de/release/arb-6.0.6/arb-6.0.6-source.tgz -> arb-6.0.6.tgz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=c13fb556a26877506fa69c3a46586bbd diff --git a/metadata/md5-cache/sci-biology/ariadne-1.3-r3 b/metadata/md5-cache/sci-biology/ariadne-1.3-r3 new file mode 100644 index 000000000000..b27761ea4fe5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ariadne-1.3-r3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 +DESCRIPTION=Protein sequences and profiles comparison +EAPI=6 +HOMEPAGE=http://www.well.ox.ac.uk/ariadne/ +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=ARIADNE +RDEPEND=>=sci-biology/ncbi-tools-0.20041020-r1 +SLOT=0 +SRC_URI=http://www.well.ox.ac.uk/ariadne/ariadne-1.3.tar.Z +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=a99266aecef97d81f48df25aa43fbb4a diff --git a/metadata/md5-cache/sci-biology/augustus-2.5.5 b/metadata/md5-cache/sci-biology/augustus-2.5.5 new file mode 100644 index 000000000000..4458afad6a1a --- /dev/null +++ b/metadata/md5-cache/sci-biology/augustus-2.5.5 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Eukaryotic gene predictor +EAPI=4 +HOMEPAGE=http://augustus.gobics.de/ +IUSE=examples +KEYWORDS=amd64 x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=5660f556708e8c3b5d43c9ef832e66ec diff --git a/metadata/md5-cache/sci-biology/bamtools-2.5.1 b/metadata/md5-cache/sci-biology/bamtools-2.5.1 new file mode 100644 index 000000000000..96eae69a4e21 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-2.5.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare setup test +DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= virtual/pkgconfig dev-util/ninja >=dev-util/cmake-3.9.6 +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=6 +HOMEPAGE=https://github.com/pezmaster31/bamtools +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +SLOT=0/2.5.1 +SRC_URI=https://github.com/pezmaster31/bamtools/archive/v2.5.1.tar.gz -> bamtools-2.5.1.tar.gz +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=283ed3269c843bce2ee0a9cefad79fe0 diff --git a/metadata/md5-cache/sci-biology/bamtools-9999 b/metadata/md5-cache/sci-biology/bamtools-9999 new file mode 100644 index 000000000000..29369b70bcf4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-9999 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= virtual/pkgconfig dev-util/ninja >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=6 +HOMEPAGE=https://github.com/pezmaster31/bamtools +IUSE=static-libs +LICENSE=MIT +RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +SLOT=0/9999 +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 git-r3 8f6de46b0aa318aea0e8cac62ece098b ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=283ed3269c843bce2ee0a9cefad79fe0 diff --git a/metadata/md5-cache/sci-biology/bcftools-1.5 b/metadata/md5-cache/sci-biology/bcftools-1.5 new file mode 100644 index 000000000000..ebe9c6a44d88 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bcftools-1.5 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-lang/perl =sci-libs/htslib-1.5*:= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] +DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files +EAPI=6 +HOMEPAGE=http://www.htslib.org +IUSE=python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=dev-lang/perl =sci-libs/htslib-1.5*:= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=https://github.com/samtools/bcftools/releases/download/1.5/bcftools-1.5.tar.bz2 +_eclasses_=multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=e289371e3fec376baf8fe36c652ca521 diff --git a/metadata/md5-cache/sci-biology/bedtools-2.26.0 b/metadata/md5-cache/sci-biology/bedtools-2.26.0 new file mode 100644 index 000000000000..86a9196345e7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bedtools-2.26.0 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install setup +DEPEND=|| ( dev-lang/python:3.6 dev-lang/python:3.5 dev-lang/python:3.4 >=dev-lang/python-2.7.5-r2:2.7 ) test? ( sci-libs/htslib sci-biology/samtools:0 ) +DESCRIPTION=Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats +EAPI=6 +HOMEPAGE=https://bedtools.readthedocs.io/ +IUSE=test +KEYWORDS=~x86 ~amd64 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib +SLOT=0 +SRC_URI=https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz https://dev.gentoo.org/~mgorny/dist/bedtools-2.26.0-fix-buildsystem.patch.bz2 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=e072d90aa6492a70f261161c8d5551e5 diff --git a/metadata/md5-cache/sci-biology/bfast-0.7.0a b/metadata/md5-cache/sci-biology/bfast-0.7.0a new file mode 100644 index 000000000000..21af40cfcc8e --- /dev/null +++ b/metadata/md5-cache/sci-biology/bfast-0.7.0a @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Blat-like Fast Accurate Search Tool +EAPI=5 +HOMEPAGE=https://sourceforge.net/projects/bfast/ +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-perl/XML-Simple +SLOT=0 +SRC_URI=mirror://sourceforge/bfast/bfast-0.7.0a.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=abc362f15c5107d96bedfb879ea0375f diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r2 b/metadata/md5-cache/sci-biology/biogrep-1.0-r2 new file mode 100644 index 000000000000..100a03ec807f --- /dev/null +++ b/metadata/md5-cache/sci-biology/biogrep-1.0-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Multithreaded tool for matching large sets of patterns against biosequence DBs +EAPI=6 +HOMEPAGE=http://stephanopoulos.openwetware.org/BIOGREP.html +IUSE=doc examples +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.openwetware.org/images/3/3d/Biogrep-1.0.tar.gz -> biogrep-1.0.tar.gz doc? ( http://www.openwetware.org/images/4/49/Biogrep.pdf -> biogrep-1.0.pdf ) +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=9731727dae2a2514bcaa486b0059272e diff --git a/metadata/md5-cache/sci-biology/biopandas-0.2.1 b/metadata/md5-cache/sci-biology/biopandas-0.2.1 new file mode 100644 index 000000000000..494606f1bfa6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopandas-0.2.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] test? ( dev-python/nose[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +DESCRIPTION=Molecular Structures in Pandas DataFrames +EAPI=6 +HOMEPAGE=https://rasbt.github.io/biopandas/ https://github.com/rasbt/biopandas https://pypi.org/project/BioPandas/ +IUSE=test python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) +SLOT=0 +SRC_URI=mirror://pypi/B/BioPandas/biopandas-0.2.1.tar.gz +_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=ea88f22f7675491064ad08658a2ba291 diff --git a/metadata/md5-cache/sci-biology/bioperl-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-1.6.9 new file mode 100644 index 000000000000..3de6735f1ef0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-1.6.9 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/YAML dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/Set-Scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Core modules +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal graphviz sqlite +db +network +run +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +PDEPEND=db? ( >=sci-biology/bioperl-db-1.6.9 ) network? ( >=sci-biology/bioperl-network-1.6.9 ) run? ( >=sci-biology/bioperl-run-1.6.9 ) +RDEPEND=dev-perl/libwww-perl !minimal? ( dev-perl/Algorithm-Munkres dev-perl/Array-Compare dev-perl/YAML dev-perl/Bio-ASN1-EntrezGene dev-perl/Clone dev-perl/Convert-Binary-C dev-perl/Data-Stag dev-perl/GD dev-perl/Graph >=dev-perl/HTML-Parser-3.60 dev-perl/List-MoreUtils dev-perl/Math-Random dev-perl/PostScript dev-perl/Set-Scalar dev-perl/SOAP-Lite dev-perl/Sort-Naturally dev-perl/Spreadsheet-ParseExcel >=virtual/perl-Storable-2.05 >=dev-perl/SVG-2.26 >=dev-perl/SVG-Graph-0.01 dev-perl/URI >=dev-perl/XML-DOM-XPath-0.13 dev-perl/XML-Parser >=dev-perl/XML-SAX-0.15 dev-perl/XML-Simple dev-perl/XML-Twig >=dev-perl/XML-Writer-0.4 dev-perl/XML-DOM dev-perl/XML-XPath ) graphviz? ( dev-perl/GraphViz ) sqlite? ( dev-perl/DBD-SQLite ) dev-lang/perl:=[-build(-)] +REQUIRED_USE=minimal? ( !graphviz ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=be22a76392a6e5c121e4b6d388045faa diff --git a/metadata/md5-cache/sci-biology/bioperl-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-9999-r1 new file mode 100644 index 000000000000..e17857bce202 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-9999-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build dev-perl/Data-Stag dev-perl/libwww-perl !minimal? ( dev-perl/Ace dev-perl/Bio-ASN1-EntrezGene dev-perl/Spreadsheet-ParseExcel dev-perl/Spreadsheet-WriteExcel >=dev-perl/XML-SAX-0.15 dev-perl/Graph dev-perl/SOAP-Lite dev-perl/Array-Compare dev-perl/SVG dev-perl/XML-Simple dev-perl/XML-Parser dev-perl/XML-Twig >=dev-perl/HTML-Parser-3.60 >=dev-perl/XML-Writer-0.4 dev-perl/Clone dev-perl/XML-DOM dev-perl/Set-Scalar dev-perl/XML-XPath dev-perl/XML-DOM-XPath dev-perl/Algorithm-Munkres dev-perl/Data-Stag dev-perl/Math-Random dev-perl/PostScript dev-perl/Convert-Binary-C dev-perl/SVG-Graph ) graphviz? ( dev-perl/GraphViz ) dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Core modules +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal graphviz +db +network +run +LICENSE=Artistic GPL-2 +PDEPEND=!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) db? ( >=sci-biology/bioperl-db-9999 ) network? ( >=sci-biology/bioperl-network-9999 ) run? ( >=sci-biology/bioperl-run-9999 ) +RDEPEND=dev-perl/Data-Stag dev-perl/libwww-perl !minimal? ( dev-perl/Ace dev-perl/Bio-ASN1-EntrezGene dev-perl/Spreadsheet-ParseExcel dev-perl/Spreadsheet-WriteExcel >=dev-perl/XML-SAX-0.15 dev-perl/Graph dev-perl/SOAP-Lite dev-perl/Array-Compare dev-perl/SVG dev-perl/XML-Simple dev-perl/XML-Parser dev-perl/XML-Twig >=dev-perl/HTML-Parser-3.60 >=dev-perl/XML-Writer-0.4 dev-perl/Clone dev-perl/XML-DOM dev-perl/Set-Scalar dev-perl/XML-XPath dev-perl/XML-DOM-XPath dev-perl/Algorithm-Munkres dev-perl/Data-Stag dev-perl/Math-Random dev-perl/PostScript dev-perl/Convert-Binary-C dev-perl/SVG-Graph ) graphviz? ( dev-perl/GraphViz ) dev-lang/perl:=[-build(-)] +SLOT=0 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=210415961127105f0fc625670ba9e423 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 new file mode 100644 index 000000000000..12bdb6098456 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=2470d7ecf1b6ff1902a8d74057748480 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 new file mode 100644 index 000000000000..f2ddddec2bfb --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-perl/Module-Build test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple ) dev-lang/perl:= +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=6 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql dev-lang/perl:= +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz +_eclasses_=multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 +_md5_=dbcb977782edcacd68dddedab8e605d9 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 new file mode 100644 index 000000000000..4972ff9cddd5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-9999-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Perl API that accesses the BioSQL schema +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +LICENSE=Artistic GPL-2 +RDEPEND=>=sci-biology/bioperl-9999 dev-perl/DBI sci-biology/biosql dev-lang/perl:=[-build(-)] +SLOT=0 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=fd4229be06b3975302e9e37ca35601d2 diff --git a/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 new file mode 100644 index 000000000000..bbca2bd83e36 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Network-1.006900.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=cb366a6a0c6cf3c12320c2d6d3551abe diff --git a/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 new file mode 100644 index 000000000000..8c77204ad407 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-network-9999-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=test +LICENSE=Artistic GPL-2 +RDEPEND=>=sci-biology/bioperl-9999 >=dev-perl/Graph-0.86 dev-lang/perl:=[-build(-)] +SLOT=0 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=025cd5fa89be402f3296160dbf755c8b diff --git a/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 new file mode 100644 index 000000000000..82aecc5602b4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] +DESCRIPTION=Perl wrapper modules for key bioinformatics applications +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal test +KEYWORDS=amd64 x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run dev-perl/File-Sort ) dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=9caec4e5b47cbf306a1689903f2a018a diff --git a/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 b/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 new file mode 100644 index 000000000000..d129942579c7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-run-9999-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-perl/Module-Build >=sci-biology/bioperl-9999 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run ) dev-lang/perl:=[-build(-)] dev-vcs/git +DESCRIPTION=Perl wrapper modules for key bioinformatics applications +EAPI=5 +HOMEPAGE=http://www.bioperl.org/ +IUSE=-minimal test +LICENSE=Artistic GPL-2 +RDEPEND=>=sci-biology/bioperl-9999 !minimal? ( dev-perl/Algorithm-Diff dev-perl/XML-Twig dev-perl/IO-String dev-perl/IPC-Run ) dev-lang/perl:=[-build(-)] +RESTRICT=test +SLOT=0 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc git-2 45ff482316b52b3f96ff6b7309b77f03 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=26abe4f8477c1a1c22bd8515484ce1c1 diff --git a/metadata/md5-cache/sci-biology/biopython-1.68 b/metadata/md5-cache/sci-biology/biopython-1.68 new file mode 100644 index 000000000000..3ac3d6de73ed --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopython-1.68 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] sys-devel/flex python_targets_pypy? ( >=virtual/pypy-5:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +DESCRIPTION=Python modules for computational molecular biology +EAPI=6 +HOMEPAGE=http://www.biopython.org/ https://pypi.org/project/biopython/ +IUSE=python_targets_pypy python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=HPND +RDEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/networkx[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/numpy[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/rdflib[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/reportlab[python_targets_python2_7(-)?,-python_single_target_python2_7(-),python_targets_python3_4(-)?,-python_single_target_python3_4(-),python_targets_python3_5(-)?,-python_single_target_python3_5(-)] dev-python/pydot[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] python_targets_pypy? ( >=virtual/pypy-5:0= ) python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) >=dev-lang/python-exec-2:=[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] +REQUIRED_USE=|| ( python_targets_pypy python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 ) +SLOT=0 +SRC_URI=http://www.biopython.org/DIST/biopython-1.68.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=d27e2e9df832a55985e7f459f9e4fa81 diff --git a/metadata/md5-cache/sci-biology/biopython-1.71 b/metadata/md5-cache/sci-biology/biopython-1.71 new file mode 100644 index 000000000000..6a370053ba13 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopython-1.71 @@ -0,0 +1,15 @@ +BDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/networkx[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/rdflib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/reportlab[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pydot[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] sys-devel/flex +DESCRIPTION=Python modules for computational molecular biology +EAPI=7 +HOMEPAGE=https://www.biopython.org/ https://pypi.org/project/biopython/ +IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=HPND +RDEPEND=dev-python/matplotlib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/networkx[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/numpy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/rdflib[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pygraphviz[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/reportlab[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/pydot[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) +SLOT=0 +SRC_URI=mirror://pypi/b/biopython/biopython-1.71.tar.gz +_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 eutils 5b8ce72259e08104b337fe28c6de5dbc multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=0227795578e2ffd9791cbebddc3ee0ab diff --git a/metadata/md5-cache/sci-biology/bioruby-1.5.1 b/metadata/md5-cache/sci-biology/bioruby-1.5.1 new file mode 100644 index 000000000000..46286a345e55 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioruby-1.5.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=test? ( ruby_targets_ruby23? ( dev-ruby/libxml[ruby_targets_ruby23] ) ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24] ) ) ruby_targets_ruby23? ( dev-lang/ruby:2.3 ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby23? ( doc? ( dev-ruby/rake[ruby_targets_ruby23] ) ) ruby_targets_ruby24? ( doc? ( dev-ruby/rake[ruby_targets_ruby24] ) ) ruby_targets_ruby23? ( test? ( dev-ruby/rake[ruby_targets_ruby23] ) ) ruby_targets_ruby24? ( test? ( dev-ruby/rake[ruby_targets_ruby24] ) ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24] ) test? ( ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24] ) ) +DESCRIPTION=An integrated environment for bioinformatics using the Ruby language +EAPI=6 +HOMEPAGE=http://bioruby.org/ +IUSE=test elibc_FreeBSD ruby_targets_ruby23 ruby_targets_ruby24 doc test test +KEYWORDS=amd64 ~ppc x86 +LICENSE=Ruby +RDEPEND=ruby_targets_ruby23? ( dev-ruby/libxml[ruby_targets_ruby23] ) ruby_targets_ruby24? ( dev-ruby/libxml[ruby_targets_ruby24] ) ruby_targets_ruby23? ( dev-lang/ruby:2.3 ) ruby_targets_ruby24? ( dev-lang/ruby:2.4 ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) ruby_targets_ruby24? ( virtual/rubygems[ruby_targets_ruby24] ) +REQUIRED_USE=|| ( ruby_targets_ruby23 ruby_targets_ruby24 ) +SLOT=0 +SRC_URI=mirror://rubygems/bio-1.5.1.gem +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 ruby-fakegem 28631ba8ae1b3218596c0eb3e38c438e ruby-ng c1f44e746d7656dd6e02d8815ff9518a ruby-utils e5942a80e3c3b936c6b84d6dc4af9f9c toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=2aecf9a558ab9d1f3e8760530ccd8e56 diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 new file mode 100644 index 000000000000..2a7fa17d9aa9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biosql-1.0.1-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install postinst +DEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) +DESCRIPTION=A generic bioinformatics relational database model +EAPI=6 +HOMEPAGE=http://www.biosql.org/ +IUSE=mysql postgres +KEYWORDS=amd64 x86 +LICENSE=LGPL-3 +RDEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) dev-lang/perl +SLOT=0 +SRC_URI=http://biosql.org/DIST/biosql-1.0.1.tar.bz2 +_md5_=c3363146ed9daed7fd12e748db91abe0 diff --git a/metadata/md5-cache/sci-biology/blat-34-r2 b/metadata/md5-cache/sci-biology/blat-34-r2 new file mode 100644 index 000000000000..c30336f803de --- /dev/null +++ b/metadata/md5-cache/sci-biology/blat-34-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DEPEND=app-arch/unzip +DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner +EAPI=6 +HOMEPAGE=http://www.cse.ucsc.edu/~kent/ +KEYWORDS=~amd64 ~x86 +LICENSE=blat +SLOT=0 +SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=d48361335699038107318f5ca57533e8 diff --git a/metadata/md5-cache/sci-biology/blossoc-1.4.0-r1 b/metadata/md5-cache/sci-biology/blossoc-1.4.0-r1 new file mode 100644 index 000000000000..877066c25789 --- /dev/null +++ b/metadata/md5-cache/sci-biology/blossoc-1.4.0-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=sci-libs/gsl:= dev-libs/boost:= sci-biology/snpfile >=sys-devel/autoconf-archive-2016.09.16 virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A linkage disequilibrium association mapping tool +EAPI=6 +HOMEPAGE=http://www.daimi.au.dk/~mailund/Blossoc/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=sci-libs/gsl:= dev-libs/boost:= sci-biology/snpfile +SLOT=0 +SRC_URI=http://www.daimi.au.dk/~mailund/Blossoc/download/blossoc-1.4.0.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=2fe1853c7621b633d2ee794ef3176e3f diff --git a/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 new file mode 100644 index 000000000000..e07e0261fe74 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-1.1.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=tbb? ( dev-cpp/tbb ) sci-biology/seqan:1.4 app-arch/unzip +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=6 +HOMEPAGE=http://bowtie-bio.sourceforge.net/ +IUSE=examples +tbb +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=Artistic +RDEPEND=tbb? ( dev-cpp/tbb ) +SLOT=1 +SRC_URI=mirror://sourceforge/bowtie-bio/bowtie-1.1.2-src.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=069dc133bc01cabadeda1e327034b7a7 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.2.9 b/metadata/md5-cache/sci-biology/bowtie-2.2.9 new file mode 100644 index 000000000000..f3b30dad12b3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-2.2.9 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install pretend +DEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) app-arch/unzip +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=6 +HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/ +IUSE=examples cpu_flags_x86_sse2 +tbb +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=dev-lang/perl tbb? ( dev-cpp/tbb ) +SLOT=2 +SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-source.zip +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=46d87c867cd445707dc1913cf3dd7eb6 diff --git a/metadata/md5-cache/sci-biology/bwa-0.7.16a b/metadata/md5-cache/sci-biology/bwa-0.7.16a new file mode 100644 index 000000000000..782a1481c347 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bwa-0.7.16a @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner +EAPI=6 +HOMEPAGE=https://bio-bwa.sourceforge.net/ +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=GPL-3 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=mirror://sourceforge/bio-bwa/bwa-0.7.16a.tar.bz2 +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=b3702a6accf64398e32e84076031919b diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6.6 b/metadata/md5-cache/sci-biology/cd-hit-4.6.6 new file mode 100644 index 000000000000..6779bec7281c --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.6.6 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install pretend setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=6 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +IUSE=openmp +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=https://github.com/weizhongli/cdhit/releases/download/V4.6.6/cd-hit-v4.6.6-2016-0711.tar.gz -> cd-hit-4.6.6.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=bbe0ae10275a73485487e08f19f4ac1b diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 new file mode 100644 index 000000000000..1cdae250f16a --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/argtable >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Scalable multiple alignment of protein sequences +EAPI=6 +HOMEPAGE=http://www.clustal.org/omega/ +IUSE=static-libs +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=dev-libs/argtable +SLOT=0 +SRC_URI=http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=9ade45d2e283bc5fcc7eef16725e18ae diff --git a/metadata/md5-cache/sci-biology/clustalw-1.83-r4 b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 new file mode 100644 index 000000000000..d8853bcdbf96 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=6 +HOMEPAGE=http://www.embl-heidelberg.de/~seqanal/ +KEYWORDS=alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=clustalw +SLOT=1 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.UNIX.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=5c8ba46cd87128b1ddae72e6ca3d07db diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1-r1 b/metadata/md5-cache/sci-biology/clustalw-2.1-r1 new file mode 100644 index 000000000000..5e8138428bfc --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-2.1-r1 @@ -0,0 +1,9 @@ +DEFINED_PHASES=install +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=6 +HOMEPAGE=http://www.clustal.org/ +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-3 LGPL-3 +SLOT=2 +SRC_URI=http://www.clustal.org/download/current/clustalw-2.1.tar.gz +_md5_=397de2c00339f3a0b847f6daa9a481fb diff --git a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 new file mode 100644 index 000000000000..c38b18613df1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=virtual/mpi +DESCRIPTION=An MPI implemention of the ClustalW general purpose multiple alignment algorithm +EAPI=6 +HOMEPAGE=http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php +IUSE=mpi_njtree static_pairalign +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=virtual/mpi +SLOT=0 +SRC_URI=http://web.bii.a-star.edu.sg/~kuobin/clustalw-mpi/clustalw-mpi-0.13.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=9e376a1d2ae782d9495b0c6c318aa097 diff --git a/metadata/md5-cache/sci-biology/clustalx-2.1-r3 b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 new file mode 100644 index 000000000000..0c6f45783eef --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 +DESCRIPTION=Graphical interface for the ClustalW multiple alignment program +EAPI=6 +HOMEPAGE=http://www.ebi.ac.uk/tools/clustalw2/ +KEYWORDS=amd64 x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 >=sci-biology/clustalw-2.1 +SLOT=0 +SRC_URI=http://www.clustal.org/download/current/clustalx-2.1.tar.gz https://dev.gentoo.org/~jlec/distfiles/clustalx.png.xz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 estack 43ddf5aaffa7a8d0482df54d25a66a1f multilib 97f470f374f2e94ccab04a2fb21d811e qmake-utils bdf97e69a34b864d6d545f4ec3143ff7 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=c8dbd602c40010526edb4955aa67e1b3 diff --git a/metadata/md5-cache/sci-biology/consed-29 b/metadata/md5-cache/sci-biology/consed-29 new file mode 100644 index 000000000000..274f6f028c74 --- /dev/null +++ b/metadata/md5-cache/sci-biology/consed-29 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install nofetch postinst prepare +DEPEND=x11-libs/libX11 x11-libs/motif:0 sci-biology/samtools:0.1-legacy virtual/pkgconfig +DESCRIPTION=A genome sequence finishing program +EAPI=6 +HOMEPAGE=http://bozeman.mbt.washington.edu/consed/consed.html +IUSE=examples +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RDEPEND=x11-libs/libX11 x11-libs/motif:0 sci-biology/samtools:0.1-legacy dev-lang/perl >=sci-biology/phred-071220-r1 >=sci-biology/phrap-1.080812-r2 +RESTRICT=fetch +SLOT=0 +SRC_URI=consed-29-sources.tar.gz consed-29-linux.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=d533d3bc63ad3989cce879478db9de97 diff --git a/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 b/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 new file mode 100644 index 000000000000..5deee9a05478 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cufflinks-2.2.1-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure prepare setup +DEPEND=sci-biology/samtools:0.1-legacy >=dev-libs/boost-1.62.0:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] dev-cpp/eigen:3 virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Transcript assembly and differential expression/regulation for RNA-Seq +EAPI=6 +HOMEPAGE=http://cufflinks.cbcb.umd.edu/ +IUSE=debug python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=sci-biology/samtools:0.1-legacy >=dev-libs/boost-1.62.0:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8e0065b0f455fa63e987f6182ed61fa1 diff --git a/metadata/md5-cache/sci-biology/cutg-160-r1 b/metadata/md5-cache/sci-biology/cutg-160-r1 new file mode 100644 index 000000000000..60c35396bc6a --- /dev/null +++ b/metadata/md5-cache/sci-biology/cutg-160-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=Codon usage tables calculated from GenBank +EAPI=5 +HOMEPAGE=http://www.kazusa.or.jp/codon/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/cutg-160.tar.xz +_md5_=bbbd347ac6eafe2416778cd68a45bf1a diff --git a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 new file mode 100644 index 000000000000..a36dedd8ac96 --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install postinst +DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment +EAPI=6 +HOMEPAGE=http://dialign-tx.gobics.de/ +KEYWORDS=~amd64 ~x86 +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=b04d9beffea802bb82f896df101ca660 diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1 new file mode 100644 index 000000000000..9c9985528a11 --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign2-2.2.1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Multiple sequence alignment +EAPI=6 +HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=3761a69a47f38308f54ae0b051361ed6 diff --git a/metadata/md5-cache/sci-biology/diya-1.0_rc4 b/metadata/md5-cache/sci-biology/diya-1.0_rc4 new file mode 100644 index 000000000000..d643878f6527 --- /dev/null +++ b/metadata/md5-cache/sci-biology/diya-1.0_rc4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple dev-lang/perl:=[-build(-)] +DESCRIPTION=Do It Yourself Annotation, tools & libraries for sequence assembly & annotation +EAPI=5 +HOMEPAGE=http://gmod.org/wiki/Diya +IUSE=-minimal +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/bioperl dev-perl/Data-Utilities dev-perl/XML-Simple !minimal? ( sci-biology/mummer sci-biology/glimmer sci-biology/trnascan-se sci-biology/infernal ) dev-lang/perl:=[-build(-)] +SLOT=0 +SRC_URI=mirror://sourceforge/diyg/files/diya/diya-1.0/diya-1.0-rc4.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 01e8c68d5a528bbcda4d3c60205983df perl-module 863b35d127db98823d439f8d73c2d011 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 unpacker 87633b2194cdb56adaa1f5a5c8862c44 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=5d4639d7c08c43e2c2208492508fd56c diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1-r1 b/metadata/md5-cache/sci-biology/elph-1.0.1-r1 new file mode 100644 index 000000000000..ce03af7423a3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/elph-1.0.1-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program +EAPI=6 +HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=dbee2f511488caf9eadadb20d043a2da diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 b/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 new file mode 100644 index 000000000000..d501a327e417 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-6.6.0-r1 @@ -0,0 +1,9 @@ +DEFINED_PHASES=- +DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons) +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/embassy/ +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=freedist +RDEPEND=>=sci-biology/embassy-cbstools-1.0.0.660 >=sci-biology/embassy-clustalomega-1.1.0.660 >=sci-biology/embassy-domainatrix-0.1.660 >=sci-biology/embassy-domalign-0.1.660 >=sci-biology/embassy-domsearch-0.1.660 >=sci-biology/embassy-emnu-1.05.660 >=sci-biology/embassy-esim4-1.0.0.660 >=sci-biology/embassy-hmmer-2.3.2.660 >=sci-biology/embassy-iprscan-4.3.1.660 >=sci-biology/embassy-meme-4.7.660 >=sci-biology/embassy-mse-3.0.0.660 >=sci-biology/embassy-phylipnew-3.69.660 >=sci-biology/embassy-signature-0.1.660 >=sci-biology/embassy-structure-0.1.660 >=sci-biology/embassy-topo-2.0.660 >=sci-biology/embassy-vienna-1.7.2.660 +SLOT=0 +_md5_=40fa8435e29624ec5b0c9ffaf2b8c695 diff --git a/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 new file mode 100644 index 000000000000..baccb8015dcb --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Applications from the CBS group +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.660.tar.gz -> embassy-cbstools-1.0.0.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=4166ba28131fdf70907b31300aa4c08b diff --git a/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 new file mode 100644 index 000000000000..fb44e625c855 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/clustal-omega dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-1.1.0.660.tar.gz -> embassy-clustalomega-1.1.0.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=ef491b452e56be12961f62b16961f4f1 diff --git a/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 new file mode 100644 index 000000000000..d90c639fdc35 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain analysis add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.660.tar.gz -> embassy-domainatrix-0.1.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=bfee4f5b2b2adadb41de2eb02d4dcbc0 diff --git a/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 new file mode 100644 index 000000000000..9e40b3a871ac --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain alignment add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.660.tar.gz -> embassy-domalign-0.1.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=9f8b2caa273f4ae3b0463e6de6782660 diff --git a/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 new file mode 100644 index 000000000000..d35d5fdbbd8f --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain search add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.660.tar.gz -> embassy-domsearch-0.1.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=920906439fbc5278460201b23a615736 diff --git a/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 new file mode 100644 index 000000000000..a52347cebf80 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Simple menu of EMBOSS applications +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=ncurses mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=ncurses? ( sys-libs/ncurses:0= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.660.tar.gz -> embassy-emnu-1.05.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=d82c7c44ec76fa5d6165769a73e5df9a diff --git a/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 new file mode 100644 index 000000000000..4c156e4ede39 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.660.tar.gz -> embassy-esim4-1.0.0.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1b156bed7ea031aeb5464836dd987f18 diff --git a/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 new file mode 100644 index 000000000000..3a606d66366e --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/hmmer:2 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.660.tar.gz -> embassy-hmmer-2.3.2.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=83d02ae22d4e1864669639d9289cd112 diff --git a/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 new file mode 100644 index 000000000000..21516fe8e442 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of InterProScan motif detection add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.660.tar.gz -> embassy-iprscan-4.3.1.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=73b0c29964ea3506d18ef6b6c8df70e1 diff --git a/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 b/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 new file mode 100644 index 000000000000..aeedd6b9ef2e --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-meme-4.7.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/meme dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.660.tar.gz -> embassy-meme-4.7.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=b18db6d7a2159272c7b69d34a14dc9b5 diff --git a/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 new file mode 100644 index 000000000000..ab994f1cc0d7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of MSE - Multiple Sequence Screen Editor +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=ncurses mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=ncurses? ( sys-libs/ncurses:0= ) dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.660.tar.gz -> embassy-mse-3.0.0.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=84df94b7c4b0f044de45cef524cbf453 diff --git a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 new file mode 100644 index 000000000000..adc1702b4f1f --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of The Phylogeny Inference Package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 freedist +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.660.tar.gz -> embassy-phylipnew-3.69.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=00620d36fbf4790dc2ecfb240ba9816c diff --git a/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 new file mode 100644 index 000000000000..31cabf1ff6a0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein signature add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.660.tar.gz -> embassy-signature-0.1.660.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 emboss-r2 e6c8236c06e1e543b4feef45c31dd618 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=4cb685046b5a39b624eb3467b815c2c4 diff --git a/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 new file mode 100644 index 000000000000..768f5143a4e2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,static-libs=,X=] +DESCRIPTION=EMBOSS integrated version of Protein structure add-on package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? 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( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +DESCRIPTION=The European Molecular Biology Open Software Suite - A sequence analysis package +EAPI=6 +HOMEPAGE=http://emboss.sourceforge.net/ +IUSE=minimal mysql pdf png postgres static-libs X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0 +PDEPEND=!minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/primer3 sci-biology/prints sci-biology/prosite sci-biology/rebase ) +RDEPEND=!games-action/xbomber !sys-devel/cons dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( virtual/mysql ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? 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( virtual/mpi sys-cluster/mpe2 ) +SLOT=0 +SRC_URI=mirror://gentoo/gibbs-3.1.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=e28918ff8ca46c8b8254e4e36f8d0bcf diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02-r3 b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 new file mode 100644 index 000000000000..541d3d024994 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmer-3.02-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=An HMM-based microbial gene finding system from 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+HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh sci-biology/elph +SLOT=0 +SRC_URI=https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=6916d92c69198563f19b744f1e57dddc diff --git a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 new file mode 100644 index 000000000000..c532987d4635 --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare unpack +DESCRIPTION=A eukaryotic gene finding system from TIGR +EAPI=4 +HOMEPAGE=http://www.cbcb.umd.edu/software/GlimmerHMM/ +KEYWORDS=amd64 x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.1.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=addae30e588a0c7a05baea53d553af0f diff --git a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 new file mode 100644 index 000000000000..735b548494bd --- /dev/null +++ b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 @@ -0,0 +1,10 @@ +DEFINED_PHASES=- +DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences +EAPI=6 +HOMEPAGE=http://research-pub.gene.com/gmap/ +KEYWORDS=~amd64 ~x86 +LICENSE=gmap +SLOT=0 +SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-12-31.v5.tar.gz +_eclasses_=estack 43ddf5aaffa7a8d0482df54d25a66a1f versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=398e7f0670f5bd07e45f2780d7fe03cf diff --git a/metadata/md5-cache/sci-biology/goby-1.9.7.3-r1 b/metadata/md5-cache/sci-biology/goby-1.9.7.3-r1 new file mode 100644 index 000000000000..242a42be0c46 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-1.9.7.3-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=>=virtual/jdk-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=A DNA sequencing data management framework +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +IUSE=+cpp elibc_FreeBSD elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=>=virtual/jre-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 cpp? ( ~sci-biology/goby-cpp-1.9.7.3 ) >=dev-java/java-config-2.2.0-r3 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-src.zip http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-deps.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-2 c4e6af2574fd1dc79b43a6e27af4b5fb java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=d8bbf59f45f0b32b55de88f3c5233883 diff --git a/metadata/md5-cache/sci-biology/goby-1.9.8.1-r1 b/metadata/md5-cache/sci-biology/goby-1.9.8.1-r1 new file mode 100644 index 000000000000..9a6f81f6f1c7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-1.9.8.1-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=>=virtual/jdk-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2 +DESCRIPTION=A DNA sequencing data management framework +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +IUSE=+cpp elibc_FreeBSD elibc_FreeBSD +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=>=virtual/jre-1.6 dev-java/commons-logging dev-java/commons-lang:2.1 dev-java/commons-io:1 dev-java/protobuf-java:0 dev-java/fastutil:0 dev-java/log4j dev-java/jsap dev-java/commons-configuration dev-java/commons-math:2 cpp? ( ~sci-biology/goby-cpp-1.9.8.1 ) >=dev-java/java-config-2.2.0-r3 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-src.zip http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-deps.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc java-ant-2 ea15ab9e838d1062abd6b53de2045d50 java-pkg-2 c4e6af2574fd1dc79b43a6e27af4b5fb java-utils-2 0ee72667014428e01a01df2345244cf3 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=d8bbf59f45f0b32b55de88f3c5233883 diff --git a/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 b/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 new file mode 100644 index 000000000000..3ac995e65ff6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-cpp-1.9.7.3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A DNA sequencing data management framework - C/C++ API +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.7.3/goby_1.9.7.3-cpp.zip +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=62b1fc794a90a87e0f80ab795108ee3c diff --git a/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 b/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 new file mode 100644 index 000000000000..d149666d18af --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-cpp-1.9.8.1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A DNA sequencing data management framework - C/C++ API +EAPI=4 +HOMEPAGE=http://campagnelab.org/software/goby/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_1.9.8.1/goby_1.9.8.1-cpp.zip +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=2599766d541e65f4acfb94c4fa4e974e diff --git a/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 b/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 new file mode 100644 index 000000000000..96facd392962 --- /dev/null +++ b/metadata/md5-cache/sci-biology/goby-cpp-2.0.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A DNA sequencing data management framework - C/C++ API +EAPI=5 +HOMEPAGE=http://campagnelab.org/software/goby/ +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=>=dev-libs/protobuf-2.4.1 >=dev-libs/libpcre-8.12 +SLOT=0 +SRC_URI=http://chagall.med.cornell.edu/goby/releases/archive/release-goby_2.0.1/goby_2.0.1-cpp.zip https://dev.gentoo.org/~mgorny/dist/goby-cpp-2.0.1-files.tar.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=8282c100b202c470aedc98e37f6151ff diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 new file mode 100644 index 000000000000..58b40abe2b1b --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r4 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install postinst +DEPEND=test? ( dev-lang/perl ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=6 +HOMEPAGE=http://hmmer.org/ +IUSE=altivec test threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=2 +SRC_URI=http://eddylab.org/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz +_md5_=2f631b79914f25875fd00c05fd144807 diff --git a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 new file mode 100644 index 000000000000..c098b0527d7b --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) test? ( dev-lang/perl ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=6 +HOMEPAGE=http://hmmer.org/ +IUSE=altivec cpu_flags_x86_sse gsl mpi test +threads +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) +SLOT=0 +SRC_URI=http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz +_md5_=e1fda24a135e4e71cdf6ae399f38faea diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r1 b/metadata/md5-cache/sci-biology/iedera-1.05-r1 new file mode 100644 index 000000000000..38c179af61ab --- /dev/null +++ b/metadata/md5-cache/sci-biology/iedera-1.05-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A subset seed design tool for DNA sequence alignment +EAPI=6 +HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=ce77e1e27bd52fed2fd2af52744d6288 diff --git a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 new file mode 100644 index 000000000000..e3d478338308 --- /dev/null +++ b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Inference of RNA alignments +EAPI=6 +HOMEPAGE=http://infernal.janelia.org/ +IUSE=mpi +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) +SLOT=0 +SRC_URI=ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz +_md5_=a3cee86cfd4ecbef4e39563bc652a64b diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 new file mode 100644 index 000000000000..975248a39250 --- /dev/null +++ b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=Important Quartet Puzzling and NNI Operation +EAPI=6 +HOMEPAGE=http://www.cibiv.at/software/iqpnni/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.cibiv.at/software/iqpnni/iqpnni-3.3.2.tar.gz +_md5_=871193b79341fc00590227fc8ec7d4d4 diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r2 b/metadata/md5-cache/sci-biology/kalign-2.03-r2 new file mode 100644 index 000000000000..57f478bea557 --- /dev/null +++ b/metadata/md5-cache/sci-biology/kalign-2.03-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Global and progressive multiple sequence alignment +EAPI=6 +HOMEPAGE=http://msa.cgb.ki.se/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://debian/pool/main/k/kalign/kalign_2.03.orig.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=175d26382226c7bed2b44be485b01d01 diff --git a/metadata/md5-cache/sci-biology/kallisto-0.43.1 b/metadata/md5-cache/sci-biology/kallisto-0.43.1 new file mode 100644 index 000000000000..6de6239d5694 --- /dev/null +++ b/metadata/md5-cache/sci-biology/kallisto-0.43.1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=sci-libs/hdf5:= sys-libs/zlib:= sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=Near-optimal RNA-Seq quantification +EAPI=6 +HOMEPAGE=http://pachterlab.github.io/kallisto/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=sci-libs/hdf5:= sys-libs/zlib:= +SLOT=0 +SRC_URI=https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz -> kallisto-0.43.1.tar.gz +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=b5fc562bf49e70db44b86bc5702ae9f2 diff --git a/metadata/md5-cache/sci-biology/kallisto-9999 b/metadata/md5-cache/sci-biology/kallisto-9999 new file mode 100644 index 000000000000..6d8f2c4a3f04 --- /dev/null +++ b/metadata/md5-cache/sci-biology/kallisto-9999 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=sci-libs/hdf5:= sys-libs/zlib:= sys-devel/make >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] +DESCRIPTION=Near-optimal RNA-Seq quantification +EAPI=6 +HOMEPAGE=http://pachterlab.github.io/kallisto/ +LICENSE=BSD +RDEPEND=sci-libs/hdf5:= sys-libs/zlib:= +SLOT=0 +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 git-r3 8f6de46b0aa318aea0e8cac62ece098b ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=b5fc562bf49e70db44b86bc5702ae9f2 diff --git a/metadata/md5-cache/sci-biology/lagan-2.0-r3 b/metadata/md5-cache/sci-biology/lagan-2.0-r3 new file mode 100644 index 000000000000..8ab697e07162 --- /dev/null +++ b/metadata/md5-cache/sci-biology/lagan-2.0-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA +EAPI=6 +HOMEPAGE=http://lagan.stanford.edu/lagan_web/index.shtml +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=http://lagan.stanford.edu/lagan_web/lagan20.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=c9dbddd6a22f2e20ff25d0aa1e6f4280 diff --git a/metadata/md5-cache/sci-biology/last-230 b/metadata/md5-cache/sci-biology/last-230 new file mode 100644 index 000000000000..a255bb1fc8fb --- /dev/null +++ b/metadata/md5-cache/sci-biology/last-230 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip +DESCRIPTION=Genome-scale comparison of biological sequences +EAPI=4 +HOMEPAGE=http://last.cbrc.jp/ +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=http://last.cbrc.jp/archive/last-230.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=5da658e6779591b0d1b9ad3413a0e7b2 diff --git a/metadata/md5-cache/sci-biology/last-299-r1 b/metadata/md5-cache/sci-biology/last-299-r1 new file mode 100644 index 000000000000..924ee2446002 --- /dev/null +++ b/metadata/md5-cache/sci-biology/last-299-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install setup +DEPEND=app-arch/unzip +DESCRIPTION=Genome-scale comparison of biological sequences +EAPI=6 +HOMEPAGE=http://last.cbrc.jp/ +IUSE=python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=http://last.cbrc.jp/last-299.zip +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=ec5206661373a6ef6ad77450dfbdb915 diff --git a/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 new file mode 100644 index 000000000000..198af655822a --- /dev/null +++ b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Gordon Text utils Library +EAPI=6 +HOMEPAGE=http://hannonlab.cshl.edu/fastx_toolkit/ +KEYWORDS=~amd64 ~x86 +LICENSE=AGPL-3 +SLOT=0/0 +SRC_URI=http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.1.tar.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=867c9b9e4eee26ad2a76ff6ff0594f52 diff --git a/metadata/md5-cache/sci-biology/mafft-7.050 b/metadata/md5-cache/sci-biology/mafft-7.050 new file mode 100644 index 000000000000..7b4bc2396e82 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mafft-7.050 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare test +DESCRIPTION=Multiple sequence alignments using a variety of algorithms +EAPI=5 +HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html +IUSE=threads +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos +LICENSE=BSD +SLOT=0 +SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.050-without-extensions-src.tgz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=3195e77c5c792018208b65f5dbeab567 diff --git a/metadata/md5-cache/sci-biology/mafft-7.215 b/metadata/md5-cache/sci-biology/mafft-7.215 new file mode 100644 index 000000000000..960656eb2384 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mafft-7.215 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare test +DESCRIPTION=Multiple sequence alignments using a variety of algorithms +EAPI=5 +HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html +IUSE=threads +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos +LICENSE=BSD +SLOT=0 +SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.215-without-extensions-src.tgz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=7b8b136195c000efff0407f671d57f19 diff --git a/metadata/md5-cache/sci-biology/mafft-7.305 b/metadata/md5-cache/sci-biology/mafft-7.305 new file mode 100644 index 000000000000..1e622db55314 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mafft-7.305 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare test +DESCRIPTION=Multiple sequence alignments using a variety of algorithms +EAPI=6 +HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html +IUSE=threads +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos +LICENSE=BSD +SLOT=0 +SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.305-without-extensions-src.tgz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=920a37021a0b392bb7315b63cf3de39d diff --git a/metadata/md5-cache/sci-biology/maq-0.7.1-r2 b/metadata/md5-cache/sci-biology/maq-0.7.1-r2 new file mode 100644 index 000000000000..cc8309cd4378 --- /dev/null +++ b/metadata/md5-cache/sci-biology/maq-0.7.1-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Mapping and Assembly with Qualities, mapping NGS reads to reference genomes +EAPI=6 +HOMEPAGE=http://maq.sourceforge.net/ +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-3 +RDEPEND=sys-libs/zlib +SLOT=0 +SRC_URI=mirror://sourceforge/maq/maq-0.7.1.tar.bz2 mirror://sourceforge/maq/calib-36.dat.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=39ffb0025210075a8d7d7f6f81f8da56 diff --git a/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 b/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 new file mode 100644 index 000000000000..407b0049f7f1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/maqview-0.2.5-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=media-libs/freeglut sys-libs/zlib >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=GUI for sci-biology/maq, a short read mapping assembler +EAPI=6 +HOMEPAGE=http://maq.sourceforge.net/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=media-libs/freeglut sys-libs/zlib sci-biology/maq +SLOT=0 +SRC_URI=mirror://sourceforge/maq/maqview-0.2.5.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=dee50558d10e75ff9e96f4c3f177c55f diff --git a/metadata/md5-cache/sci-biology/mcl-08.312 b/metadata/md5-cache/sci-biology/mcl-08.312 new file mode 100644 index 000000000000..a0c07208af25 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mcl-08.312 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A Markov Cluster Algorithm implementation +EAPI=4 +HOMEPAGE=http://micans.org/mcl/ +IUSE=+blast +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://micans.org/mcl/src/mcl-08-312.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=24cf3aad7375304f2721048d2f76b5f1 diff --git a/metadata/md5-cache/sci-biology/mcl-12.135 b/metadata/md5-cache/sci-biology/mcl-12.135 new file mode 100644 index 000000000000..e4d6b16efd80 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mcl-12.135 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A Markov Cluster Algorithm implementation +EAPI=4 +HOMEPAGE=http://micans.org/mcl/ +IUSE=+blast +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://micans.org/mcl/src/mcl-12-135.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 autotools-utils 5a4611dfba155b1659528663fad4cd5e desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=24cf3aad7375304f2721048d2f76b5f1 diff --git a/metadata/md5-cache/sci-biology/mcl-14.137 b/metadata/md5-cache/sci-biology/mcl-14.137 new file mode 100644 index 000000000000..c01e319373af --- /dev/null +++ b/metadata/md5-cache/sci-biology/mcl-14.137 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure prepare +DEPEND=>=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A Markov Cluster Algorithm implementation +EAPI=6 +HOMEPAGE=http://micans.org/mcl/ +IUSE=+blast +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://micans.org/mcl/src/mcl-14-137.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=3429c68609b6c70e047d577379f68f97 diff --git a/metadata/md5-cache/sci-biology/meme-4.11.2_p2 b/metadata/md5-cache/sci-biology/meme-4.11.2_p2 new file mode 100644 index 000000000000..dc8a8300e1c3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/meme-4.11.2_p2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare setup test +DEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] app-shells/tcsh dev-libs/libxml2:2 dev-libs/libxslt sys-libs/zlib app-text/ghostscript-gpl media-gfx/imagemagick dev-lang/perl:= dev-perl/HTML-Parser dev-perl/HTML-Template dev-perl/Log-Log4perl dev-perl/Math-CDF dev-perl/XML-Compile-SOAP dev-perl/XML-Compile-WSDL11 dev-perl/XML-Parser dev-perl/XML-Simple virtual/perl-Data-Dumper virtual/perl-Exporter virtual/perl-File-Path virtual/perl-File-Spec virtual/perl-File-Temp virtual/perl-Getopt-Long virtual/perl-Scalar-List-Utils virtual/perl-Time-HiRes mpi? ( virtual/mpi ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=The MEME/MAST system - Motif discovery and search +EAPI=6 +HOMEPAGE=http://meme-suite.org/tools/meme +IUSE=debug doc examples mpi python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=meme +RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] app-shells/tcsh dev-libs/libxml2:2 dev-libs/libxslt sys-libs/zlib app-text/ghostscript-gpl media-gfx/imagemagick dev-lang/perl:= dev-perl/HTML-Parser dev-perl/HTML-Template dev-perl/Log-Log4perl dev-perl/Math-CDF dev-perl/XML-Compile-SOAP dev-perl/XML-Compile-WSDL11 dev-perl/XML-Parser dev-perl/XML-Simple virtual/perl-Data-Dumper virtual/perl-Exporter virtual/perl-File-Path virtual/perl-File-Spec virtual/perl-File-Temp virtual/perl-Getopt-Long virtual/perl-Scalar-List-Utils virtual/perl-Time-HiRes mpi? ( virtual/mpi ) +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=http://meme-suite.org/meme-software/4.11.2/meme_4.11.2.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 estack 43ddf5aaffa7a8d0482df54d25a66a1f libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e perl-functions 01e8c68d5a528bbcda4d3c60205983df python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=a4080439675628436c06de8db9f59c6e diff --git a/metadata/md5-cache/sci-biology/mira-4.0.2 b/metadata/md5-cache/sci-biology/mira-4.0.2 new file mode 100644 index 000000000000..c3ab2984c38f --- /dev/null +++ b/metadata/md5-cache/sci-biology/mira-4.0.2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install postinst prepare +DEPEND=dev-libs/boost[threads] dev-util/google-perftools sys-devel/flex app-editors/vim-core dev-libs/expat >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina +EAPI=6 +HOMEPAGE=http://www.chevreux.org/projects_mira.html +IUSE=doc +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~x86-macos +LICENSE=GPL-2 +RDEPEND=dev-libs/boost[threads] dev-util/google-perftools +SLOT=0 +SRC_URI=https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira-4.0.2.tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_06-07-2012.tar.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=4e9fc8a550640febbc0b71544c16618c diff --git a/metadata/md5-cache/sci-biology/mosaik-2.2.30 b/metadata/md5-cache/sci-biology/mosaik-2.2.30 new file mode 100644 index 000000000000..2b31348a3ea9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mosaik-2.2.30 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile configure install unpack +DESCRIPTION=A reference-guided aligner for next-generation sequencing technologies +EAPI=6 +HOMEPAGE=https://github.com/wanpinglee/MOSAIK +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> mosaik-2.2.30.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf vcs-snapshot 3be1ab44131e8c0bbdaa75823008444b +_md5_=630686b35f8a549c580c5fd0e2cb02fc diff --git a/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 new file mode 100644 index 000000000000..bb76d8a95324 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=sci-biology/uchime mpi? ( virtual/mpi ) app-arch/unzip virtual/fortran +DESCRIPTION=A suite of algorithms for ecological bioinformatics +EAPI=5 +HOMEPAGE=https://www.mothur.org/ +IUSE=mpi +readline +KEYWORDS=amd64 x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran +SLOT=0 +SRC_URI=https://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 fortran-2 9e7f20c99213f0627ff7f873d4aaa25d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=17f8b3c73710bbb746fc4cbfcf78b85d diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 new file mode 100644 index 000000000000..dd5bd27cc2f2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=4 +HOMEPAGE=http://mrbayes.csit.fsu.edu/ +IUSE=debug mpi readline +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) +SLOT=0 +SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=a082c9b1f1b5f9fa9b85e23eb7009a6d diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 new file mode 100644 index 000000000000..8cdce0ea72ba --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=5 +HOMEPAGE=http://mrbayes.csit.fsu.edu/ +IUSE=debug mpi readline +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses:0= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= ) +SLOT=0 +SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=a944448f568e57bb9f221cd1f437ab09 diff --git a/metadata/md5-cache/sci-biology/mummer-3.23 b/metadata/md5-cache/sci-biology/mummer-3.23 new file mode 100644 index 000000000000..46151624c2bb --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.23 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A rapid whole genome aligner +EAPI=6 +HOMEPAGE=http://mummer.sourceforge.net/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh dev-lang/perl +SLOT=0 +SRC_URI=mirror://sourceforge/mummer/MUMmer3.23.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=c256f298b416306c1be7005e7877f7b9 diff --git a/metadata/md5-cache/sci-biology/muscle-3.8.31 b/metadata/md5-cache/sci-biology/muscle-3.8.31 new file mode 100644 index 000000000000..4e5e149ac328 --- /dev/null +++ b/metadata/md5-cache/sci-biology/muscle-3.8.31 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Multiple sequence comparison by log-expectation +EAPI=5 +HOMEPAGE=http://www.drive5.com/muscle/ +KEYWORDS=amd64 ppc x86 +LICENSE=public-domain +RDEPEND=!sci-libs/libmuscle +SLOT=0 +SRC_URI=http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=500ff424aff8c56744362bc87a3ff285 diff --git a/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 new file mode 100644 index 000000000000..04c9fa3b90c9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/ncbi-tools-2.2.26-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) +DESCRIPTION=Development toolkit and applications for computational biology, including BLAST +EAPI=5 +HOMEPAGE=https://www.ncbi.nlm.nih.gov/ +IUSE=doc static-libs X +KEYWORDS=~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=public-domain +RDEPEND=app-shells/tcsh dev-lang/perl media-libs/libpng:0= X? ( media-libs/fontconfig x11-libs/motif:0= x11-libs/libICE x11-libs/libX11 x11-libs/libXft x11-libs/libXmu x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/ncbi.tar.gz -> ncbi-tools-2.2.26.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=550e2f5b19e400b1ca82a7ba4f7bd44a diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6 b/metadata/md5-cache/sci-biology/newick-utils-1.6 new file mode 100644 index 000000000000..f9cdb1fd46cd --- /dev/null +++ b/metadata/md5-cache/sci-biology/newick-utils-1.6 @@ -0,0 +1,10 @@ +DEFINED_PHASES=test +DESCRIPTION=Tools for processing phylogenetic trees +EAPI=6 +HOMEPAGE=http://cegg.unige.ch/newick_utils +KEYWORDS=~amd64 ~x86 +LICENSE=BSD +RDEPEND=!dev-games/libnw +SLOT=0 +SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz +_md5_=f70356a582d317400bf4cd17b73beb16 diff --git a/metadata/md5-cache/sci-biology/njplot-2.3-r2 b/metadata/md5-cache/sci-biology/njplot-2.3-r2 new file mode 100644 index 000000000000..3eab09436b34 --- /dev/null +++ b/metadata/md5-cache/sci-biology/njplot-2.3-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=install prepare +DEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +DESCRIPTION=A phylogenetic tree drawing program which supports tree rooting +EAPI=6 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/njplot.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=sci-biology/ncbi-tools[X,static-libs] x11-libs/libXmu +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-2.3.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=c70b49c7f5e1a92f5169df372f9638c6 diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r1 b/metadata/md5-cache/sci-biology/pals-1.0-r1 new file mode 100644 index 000000000000..c1ca8de69a5e --- /dev/null +++ b/metadata/md5-cache/sci-biology/pals-1.0-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Pairwise Aligner for Long Sequences +EAPI=6 +HOMEPAGE=http://www.drive5.com/pals/ +KEYWORDS=amd64 x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=http://www.drive5.com/pals/pals_source.tar.gz -> pals-1.0.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=b0df20d47905df6a290c5fe2f79fd48b diff --git a/metadata/md5-cache/sci-biology/paml-4.4c-r1 b/metadata/md5-cache/sci-biology/paml-4.4c-r1 new file mode 100644 index 000000000000..b1b9e039c32a --- /dev/null +++ b/metadata/md5-cache/sci-biology/paml-4.4c-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Phylogenetic Analysis by Maximum Likelihood +EAPI=5 +HOMEPAGE=http://abacus.gene.ucl.ac.uk/software/paml.html +KEYWORDS=amd64 x86 +LICENSE=free-noncomm +SLOT=0 +SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.4c.tar.gz +_eclasses_=estack 43ddf5aaffa7a8d0482df54d25a66a1f multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=c46d709378282d4ccbb567aaa00ee01a diff --git a/metadata/md5-cache/sci-biology/phrap-1.080812-r2 b/metadata/md5-cache/sci-biology/phrap-1.080812-r2 new file mode 100644 index 000000000000..ab42e7852a47 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phrap-1.080812-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install nofetch +DESCRIPTION=Shotgun assembly and alignment utilities +EAPI=6 +HOMEPAGE=http://www.phrap.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RDEPEND=dev-lang/perl dev-perl/Tk +RESTRICT=fetch +SLOT=0 +SRC_URI=phrap-1.080812-distrib.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=e72f3e08accb23ebf55562689dad5f46 diff --git a/metadata/md5-cache/sci-biology/phred-071220-r1 b/metadata/md5-cache/sci-biology/phred-071220-r1 new file mode 100644 index 000000000000..6b7893cd8fd6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phred-071220-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install nofetch +DESCRIPTION=A base caller for Sanger DNA sequencing +EAPI=6 +HOMEPAGE=http://phrap.org/phredphrapconsed.html +KEYWORDS=~amd64 ~x86 +LICENSE=phrap +RESTRICT=fetch +SLOT=0 +SRC_URI=phred-dist-071220.b-acd.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=92065ca72fd55796ea38e3d5ae9ee8b8 diff --git a/metadata/md5-cache/sci-biology/phylip-3.69-r1 b/metadata/md5-cache/sci-biology/phylip-3.69-r1 new file mode 100644 index 000000000000..4acb8033a5b3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.69-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=freedist +RDEPEND=x11-libs/libXaw +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=d0432dd24ac4208e4dfcf91bea60d018 diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r1 b/metadata/md5-cache/sci-biology/phylip-3.696-r1 new file mode 100644 index 000000000000..cf3162ed87c1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.696-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=BSD-2 +RDEPEND=x11-libs/libXaw +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=8b5da2d13bfc622e3156ee011204f899 diff --git a/metadata/md5-cache/sci-biology/phylip-3.696-r2 b/metadata/md5-cache/sci-biology/phylip-3.696-r2 new file mode 100644 index 000000000000..95ebdd29ef73 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.696-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=x11-libs/libXaw !!dev-lang/elixir x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=5 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=BSD-2 +RDEPEND=x11-libs/libXaw !!dev-lang/elixir +SLOT=0 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( virtual/pkgconfig ) +DESCRIPTION=Whole genome association analysis toolset +EAPI=4 +HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ +IUSE=lapack -webcheck R +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib lapack? ( virtual/lapack ) +SLOT=0 +SRC_URI=http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=b659cc5ab8af123ceaf15f1349214345 diff --git a/metadata/md5-cache/sci-biology/plink-1.90_pre140514 b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 new file mode 100644 index 000000000000..e6a25114c67e --- /dev/null +++ b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=app-arch/unzip virtual/pkgconfig +DESCRIPTION=Whole genome association analysis toolset +EAPI=5 +HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib virtual/cblas virtual/lapack +SLOT=0 +SRC_URI=http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> plink-1.90_pre140514.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=570249dc23feeff7b47b3e81df358196 diff --git a/metadata/md5-cache/sci-biology/poa-2-r1 b/metadata/md5-cache/sci-biology/poa-2-r1 new file mode 100644 index 000000000000..4e911ec2aa18 --- /dev/null +++ b/metadata/md5-cache/sci-biology/poa-2-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Fast multiple sequence alignments using partial-order graphs +EAPI=5 +HOMEPAGE=http://bioinfo.mbi.ucla.edu/poa/ +IUSE=static-libs +KEYWORDS=~x86 ~amd64 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/poamsa/poaV2.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=4f0b8d6c2192465644af4890a995d48a diff --git a/metadata/md5-cache/sci-biology/prank-140603 b/metadata/md5-cache/sci-biology/prank-140603 new file mode 100644 index 000000000000..16126944bac3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-140603 @@ -0,0 +1,10 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Probabilistic Alignment Kit +EAPI=6 +HOMEPAGE=http://wasabiapp.org/software/prank/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=17023476000980284365a9c0ed04a6f0 diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.7 b/metadata/md5-cache/sci-biology/primer3-2.3.7 new file mode 100644 index 000000000000..adbd3096ef58 --- /dev/null +++ b/metadata/md5-cache/sci-biology/primer3-2.3.7 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-lang/perl +DESCRIPTION=Primer Design for PCR reactions +EAPI=6 +HOMEPAGE=http://primer3.sourceforge.net/ +KEYWORDS=~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/project/primer3/primer3/2.3.7/primer3-2.3.7.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=e79ee4774138e651c83467c2b2cb2926 diff --git a/metadata/md5-cache/sci-biology/prints-39.0-r1 b/metadata/md5-cache/sci-biology/prints-39.0-r1 new file mode 100644 index 000000000000..31cee51db19f --- /dev/null +++ b/metadata/md5-cache/sci-biology/prints-39.0-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? 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( sci-biology/emboss ) +DESCRIPTION=A protein families and domains database +EAPI=6 +HOMEPAGE=https://prosite.expasy.org/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=ftp://ftp.expasy.org/databases/prosite/old_releases/prosite2017_02.tar.bz2 +_md5_=e37bd9f81e9458715d22a6138fb2029a diff --git a/metadata/md5-cache/sci-biology/psipred-3.2.1 b/metadata/md5-cache/sci-biology/psipred-3.2.1 new file mode 100644 index 000000000000..c85593c128c3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.2.1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=4 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred321.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=bf7aa50ff789d669fe4846e0e41828d7 diff --git a/metadata/md5-cache/sci-biology/psipred-3.3 b/metadata/md5-cache/sci-biology/psipred-3.3 new file mode 100644 index 000000000000..d2087ae3d6f7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=4 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.3.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=d719359ecbbd5c0825e93788cc4f0af1 diff --git a/metadata/md5-cache/sci-biology/psipred-3.4 b/metadata/md5-cache/sci-biology/psipred-3.4 new file mode 100644 index 000000000000..d60214127cf0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.4 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=5 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=app-shells/tcsh sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.4.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=671e20dbd509ebdd9e9c492e2c53b6a1 diff --git a/metadata/md5-cache/sci-biology/psipred-3.5 b/metadata/md5-cache/sci-biology/psipred-3.5 new file mode 100644 index 000000000000..b55a418b2480 --- /dev/null +++ b/metadata/md5-cache/sci-biology/psipred-3.5 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst prepare +DESCRIPTION=Protein Secondary Structure Prediction +EAPI=5 +HOMEPAGE=http://bioinf.cs.ucl.ac.uk/psipred/ +IUSE=test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=psipred +RDEPEND=app-shells/tcsh sci-biology/ncbi-tools || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) +SLOT=0 +SRC_URI=http://bioinf.cs.ucl.ac.uk/downloads/psipred/psipred3.5.tar.gz test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz ) +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e prefix e51c7882b7b721e54e684f7eb143cbfe preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=671e20dbd509ebdd9e9c492e2c53b6a1 diff --git a/metadata/md5-cache/sci-biology/pysam-0.12.0.1 b/metadata/md5-cache/sci-biology/pysam-0.12.0.1 new file mode 100644 index 000000000000..06894319482d --- /dev/null +++ b/metadata/md5-cache/sci-biology/pysam-0.12.0.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND==sci-libs/htslib-1.5*:= dev-python/cython[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format +EAPI=6 +HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/ +IUSE=python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND==sci-libs/htslib-1.5*:= python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_4? ( dev-lang/python:3.4 ) python_targets_python3_5? ( dev-lang/python:3.5 ) python_targets_python3_6? ( dev-lang/python:3.6 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] +REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 python_targets_python3_6 ) +SLOT=0 +SRC_URI=mirror://pypi/p/pysam/pysam-0.12.0.1.tar.gz +_eclasses_=distutils-r1 63fea93ca1cc4fdc5fa2247afc4e3a15 multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=c02049dd445007999f7534a8e5d17656 diff --git a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 new file mode 100644 index 000000000000..d7019e7fcb07 --- /dev/null +++ b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DEPEND=dev-lang/perl sci-biology/hmmer:2 +DESCRIPTION=Prototype ncRNA genefinder +EAPI=6 +HOMEPAGE=http://selab.janelia.org/software.html +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl sci-biology/hmmer:2 +SLOT=0 +SRC_URI=mirror://gentoo/qrna-2.0.3c.tar.bz2 +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=0fc8dac0f54d22c60da996470b3b33ee diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-7.2.6 new file mode 100644 index 000000000000..d71204ce3c6a --- /dev/null +++ b/metadata/md5-cache/sci-biology/raxml-7.2.6 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees +EAPI=5 +HOMEPAGE=http://wwwkramer.in.tum.de/exelixis/software.html +IUSE=cpu_flags_x86_sse3 +threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +REQUIRED_USE=cpu_flags_x86_sse3 +SLOT=0 +SRC_URI=http://wwwkramer.in.tum.de/exelixis/software/RAxML-7.2.6.tar.bz2 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=f2b8e0b4e5701d9b20bcbf9151c9b868 diff --git a/metadata/md5-cache/sci-biology/rebase-1701 b/metadata/md5-cache/sci-biology/rebase-1701 new file mode 100644 index 000000000000..d86bf89d9ab9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1701 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1701.tar.xz +_md5_=68457638d36f4995a29fb959283e85a4 diff --git a/metadata/md5-cache/sci-biology/rebase-1702 b/metadata/md5-cache/sci-biology/rebase-1702 new file mode 100644 index 000000000000..b16c62f4e2fa --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1702 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1702.tar.xz +_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1703 b/metadata/md5-cache/sci-biology/rebase-1703 new file mode 100644 index 000000000000..5172f9e323ca --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1703 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1703.tar.xz +_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1704 b/metadata/md5-cache/sci-biology/rebase-1704 new file mode 100644 index 000000000000..4165b701add8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1704 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1704.tar.xz +_md5_=b934757ccdbd2999376f90a29fabbeb5 diff --git a/metadata/md5-cache/sci-biology/rebase-1803 b/metadata/md5-cache/sci-biology/rebase-1803 new file mode 100644 index 000000000000..e04f8ae6b53d --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1803 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1803.tar.xz +_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/rebase-1806 b/metadata/md5-cache/sci-biology/rebase-1806 new file mode 100644 index 000000000000..8eeafd55e477 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1806 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +DESCRIPTION=A restriction enzyme database +EAPI=6 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris +LICENSE=public-domain +RDEPEND=emboss? ( >=sci-biology/emboss-5.0.0 ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1806.tar.xz +_md5_=03338bf80d0fb82894ab8e39e00b1898 diff --git a/metadata/md5-cache/sci-biology/recon-1.08 b/metadata/md5-cache/sci-biology/recon-1.08 new file mode 100644 index 000000000000..47eba7fb8c90 --- /dev/null +++ b/metadata/md5-cache/sci-biology/recon-1.08 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Automated de novo identification of repeat families from genomic sequences +EAPI=6 +HOMEPAGE=http://www.repeatmasker.org/RepeatModeler.html +IUSE=examples +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RECON-1.08.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=2ddd537d912c7c88b6f0b0d203a51613 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 new file mode 100644 index 000000000000..dd6911f77a84 --- /dev/null +++ b/metadata/md5-cache/sci-biology/repeatmasker-4.0.1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Screen DNA sequences for interspersed repeats and low complexity DNA +EAPI=5 +HOMEPAGE=http://repeatmasker.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=OSL-2.1 +RDEPEND=sci-biology/rmblast sci-biology/trf sci-biology/repeatmasker-libraries +SLOT=0 +SRC_URI=http://www.repeatmasker.org/RepeatMasker-open-4-0-1.tar.gz +_md5_=9dc3465c819cad44a5a8175a267222d4 diff --git a/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 new file mode 100644 index 000000000000..3f4cf1c19817 --- /dev/null +++ b/metadata/md5-cache/sci-biology/repeatmasker-libraries-20120418 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install nofetch +DESCRIPTION=A special version of RepBase used by RepeatMasker +EAPI=5 +HOMEPAGE=http://repeatmasker.org/ +KEYWORDS=~amd64 ~x86 +LICENSE=all-rights-reserved +RESTRICT=fetch +SLOT=0 +SRC_URI=repeatmaskerlibraries-20120418.tar.gz +_md5_=0cb0252babed9e448a9b2b06eaa2220c diff --git a/metadata/md5-cache/sci-biology/rmblast-1.2-r1 b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 new file mode 100644 index 000000000000..84990ee30ed3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rmblast-1.2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure prepare +DEPEND=dev-libs/boost app-arch/cpio +DESCRIPTION=RepeatMasker compatible version of NCBI BLAST+ +EAPI=5 +HOMEPAGE=http://www.repeatmasker.org/RMBlast.html +KEYWORDS=~amd64 ~x86 +LICENSE=OSL-2.1 +RDEPEND=dev-libs/boost +SLOT=0 +SRC_URI=http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz https://dev.gentoo.org/~mgorny/dist/rmblast-1.2-gcc47.patch.bz2 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1283e94bf3a231a794a498d2769aaa7d diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r4 b/metadata/md5-cache/sci-biology/rnaview-20040713-r4 new file mode 100644 index 000000000000..f0e81c01d7d9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r4 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=6 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=788c156d45287bef4f6aa876055bde4c diff --git a/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 b/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 new file mode 100644 index 000000000000..e2658d0f437d --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-0.1.20-r3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare setup +DEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] sys-libs/ncurses:0= dev-lang/perl virtual/pkgconfig +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=6 +HOMEPAGE=http://samtools.sourceforge.net/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] sys-libs/ncurses:0= dev-lang/perl +REQUIRED_USE=python_targets_python2_7 +SLOT=0.1-legacy +SRC_URI=https://github.com/samtools/samtools/archive/0.1.20.tar.gz -> samtools-0.1.20.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=fa48f0b2be780a9264eb9d727ec53335 diff --git a/metadata/md5-cache/sci-biology/samtools-1.5 b/metadata/md5-cache/sci-biology/samtools-1.5 new file mode 100644 index 000000000000..ddc79a71da47 --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.5 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare test +DEPEND=dev-lang/perl =sci-libs/htslib-1.5* sys-libs/ncurses:0= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=6 +HOMEPAGE=http://www.htslib.org/ +IUSE=examples python_targets_python2_7 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=dev-lang/perl =sci-libs/htslib-1.5* sys-libs/ncurses:0= sys-libs/zlib python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] +REQUIRED_USE=|| ( python_targets_python2_7 ) +SLOT=0 +SRC_URI=mirror://sourceforge/samtools/samtools-1.5.tar.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e python-r1 0b5829eb6369d7af3a834b6eed7b7107 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=8d92b4a814f62eab87bac2be22c2470c diff --git a/metadata/md5-cache/sci-biology/seaview-4.3.5 b/metadata/md5-cache/sci-biology/seaview-4.3.5 new file mode 100644 index 000000000000..f0dfa48c04a0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.3.5 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.3.5.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=38cc02682d853c813df2b6e81cbb51c5 diff --git a/metadata/md5-cache/sci-biology/seaview-4.5.4 b/metadata/md5-cache/sci-biology/seaview-4.5.4 new file mode 100644 index 000000000000..969930293946 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.5.4 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=5 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=amd64 x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.4.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=38cc02682d853c813df2b6e81cbb51c5 diff --git a/metadata/md5-cache/sci-biology/seaview-4.6 b/metadata/md5-cache/sci-biology/seaview-4.6 new file mode 100644 index 000000000000..b71aeb30d146 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.6 @@ -0,0 +1,13 @@ +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw:2 || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml virtual/pkgconfig +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=6 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +IUSE=+xft +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw:2 || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.6.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=1a6723f1ab0e67cc0d63dd54a902900f diff --git a/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 new file mode 100644 index 000000000000..d271928f2239 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install postinst prepare setup test +DEPEND=app-arch/bzip2 sys-libs/zlib test? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/nose[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 test +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2 sys-libs/zlib +REQUIRED_USE=cpu_flags_x86_sse4_1 +SLOT=1.4 +SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-1.4.2.tar.gz +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=1b7be060ecec73f1e66596a71b90a92a diff --git a/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 b/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 new file mode 100644 index 000000000000..8fdfb31f8f85 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-2.2.0-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare setup test +DEPEND=app-arch/bzip2 sys-libs/zlib !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) test? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/nose[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2 sys-libs/zlib !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 +REQUIRED_USE=cpu_flags_x86_sse4_1 +SLOT=0 +SRC_URI=http://packages.seqan.de/seqan-src/seqan-src-2.2.0.tar.gz +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf versionator 26ca8a8bd95d6a74122c08ba98a4ee72 xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=aaf78a04252c5e6c2b92b04c7211b73c diff --git a/metadata/md5-cache/sci-biology/seqan-2.4.0 b/metadata/md5-cache/sci-biology/seqan-2.4.0 new file mode 100644 index 000000000000..884771733521 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-2.4.0 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare setup test +DEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) dev-util/ninja >=dev-util/cmake-3.9.6 +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc tools +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 +REQUIRED_USE=cpu_flags_x86_sse4_1 +SLOT=0 +SRC_URI=https://github.com/seqan/seqan/archive/seqan-v2.4.0.tar.gz +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=ca34cde2b2fc2f8692469a016bc077f6 diff --git a/metadata/md5-cache/sci-biology/seqan-9999 b/metadata/md5-cache/sci-biology/seqan-9999 new file mode 100644 index 000000000000..d9b2e95cf64f --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-9999 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare setup test unpack +DEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 doc? ( || ( ( >=dev-lang/python-2.7.5-r2:2.7 dev-python/sphinx[python_targets_python2_7(-),python_single_target_python2_7(+)] ) ) || ( >=dev-lang/python-2.7.5-r2:2.7 ) ) dev-util/ninja >=dev-util/cmake-3.9.6 >=dev-vcs/git-1.8.2.1[curl] +DESCRIPTION=C++ Sequence Analysis Library +EAPI=6 +HOMEPAGE=http://www.seqan.de/ +IUSE=cpu_flags_x86_sse4_1 doc tools +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2:= sys-libs/zlib:= !!sci-biology/seqan:2.0 !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2 +REQUIRED_USE=cpu_flags_x86_sse4_1 +SLOT=0 +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 git-r3 8f6de46b0aa318aea0e8cac62ece098b ltprune 607e058da37aa6dabfa408b7d61da72e multibuild 35719a9cd25ec71ee49c966f6868454c multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 python-any-r1 6faea633ae2f79f6d55dcfd431b79fbf python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=954c2a9b05e60f6a61eb27c1cc720117 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.0.1 b/metadata/md5-cache/sci-biology/shrimp-2.0.1 new file mode 100644 index 000000000000..09c3c171924f --- /dev/null +++ b/metadata/md5-cache/sci-biology/shrimp-2.0.1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare setup +DEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs +DESCRIPTION=SHort Read Mapping Package +EAPI=4 +HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ +IUSE=custom-cflags +KEYWORDS=amd64 x86 +LICENSE=shrimp +RDEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs +SLOT=0 +SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_0_1.src.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=33caa30e4cdcb3e86f4b1be8c6c30c46 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.2.3 b/metadata/md5-cache/sci-biology/shrimp-2.2.3 new file mode 100644 index 000000000000..ce7d3554c1ab --- /dev/null +++ b/metadata/md5-cache/sci-biology/shrimp-2.2.3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare pretend setup +DEPEND=!sci-mathematics/cado-nfs +DESCRIPTION=SHort Read Mapping Package +EAPI=5 +HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ +IUSE=custom-cflags +cpu_flags_x86_sse2 python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=shrimp +RDEPEND=!sci-mathematics/cado-nfs python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_3.src.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=98a7a2b9765ad5e245b1b7b9be67060b diff --git a/metadata/md5-cache/sci-biology/sibsim4-0.20 b/metadata/md5-cache/sci-biology/sibsim4-0.20 new file mode 100644 index 000000000000..dce86b046849 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sibsim4-0.20 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=A rewrite and improvement upon sim4, a DNA-mRNA aligner +EAPI=5 +HOMEPAGE=http://sibsim4.sourceforge.net/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/sibsim4/SIBsim4-0.20.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=84a29c8972011ec4b86f3c8235a7b5d2 diff --git a/metadata/md5-cache/sci-biology/sim4-20030921-r2 b/metadata/md5-cache/sci-biology/sim4-20030921-r2 new file mode 100644 index 000000000000..6d0cdfcf5f81 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sim4-20030921-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A program to align cDNA and genomic DNA +EAPI=6 +HOMEPAGE=http://globin.cse.psu.edu/html/docs/sim4.html +KEYWORDS=~amd64 ~ppc ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=fca00baca723bafd7976eff8dccc5c26 diff --git a/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2 b/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2 new file mode 100644 index 000000000000..eee0b602f033 --- /dev/null +++ b/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/boost:= >=sys-devel/autoconf-archive-2016.09.16 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A library and API for manipulating large SNP datasets +EAPI=6 +HOMEPAGE=http://www.birc.au.dk/~mailund/SNPFile/ +IUSE=static-libs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=dev-libs/boost:= +SLOT=0 +SRC_URI=http://www.birc.au.dk/~mailund/SNPFile/download/snpfile-2.0.1.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=7c64014825a157024d03614c037abcfc diff --git a/metadata/md5-cache/sci-biology/stride-20011129-r1 b/metadata/md5-cache/sci-biology/stride-20011129-r1 new file mode 100644 index 000000000000..e3aa3af0fd8f --- /dev/null +++ b/metadata/md5-cache/sci-biology/stride-20011129-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install prepare +DESCRIPTION=Protein secondary structure assignment from atomic coordinates +EAPI=5 +HOMEPAGE=http://webclu.bio.wzw.tum.de/stride/ +KEYWORDS=amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos +LICENSE=STRIDE +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/stride.tar.gz https://dev.gentoo.org/~jlec/distfiles/stride-20060723-update.patch.bz2 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=d73db26f06440dc2c2a1e25befe5d490 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 new file mode 100644 index 000000000000..5ada2e982e45 --- /dev/null +++ b/metadata/md5-cache/sci-biology/t-coffee-11.00-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=A multiple sequence alignment package +EAPI=6 +HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html +KEYWORDS=~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=sci-biology/clustalw sci-chemistry/tm-align +SLOT=0 +SRC_URI=http://www.tcoffee.org/Packages/Beta/Latest/T-COFFEE_distribution_Version_11.00.4466924.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=5c54b109c5b8bef93adbc5f99ddd7114 diff --git a/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 b/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 new file mode 100644 index 000000000000..e52b949b6516 --- /dev/null +++ b/metadata/md5-cache/sci-biology/tophat-2.1.1-r4 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install postinst prepare setup +DEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] dev-libs/boost:=[threads] dev-python/intervaltree[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] dev-python/sortedcontainers[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 virtual/pkgconfig sci-biology/seqan:1.4 >=sys-devel/autoconf-archive-2016.09.16 >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Python-based splice junction mapper for RNA-Seq reads using bowtie2 +EAPI=6 +HOMEPAGE=https://ccb.jhu.edu/software/tophat/ +IUSE=debug python_targets_python2_7 +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] dev-libs/boost:=[threads] dev-python/intervaltree[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] dev-python/sortedcontainers[python_targets_python2_7(-)?,-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2 +REQUIRED_USE=python_targets_python2_7 +SLOT=0 +SRC_URI=https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 python-single-r1 26fdbe5e685d53f67303a3a43d9e4848 python-utils-r1 7db901256449fef43c3aaa4d486c1c63 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=efee8069c83c578acac8e57b429ad985 diff --git a/metadata/md5-cache/sci-biology/transfac-3.2-r1 b/metadata/md5-cache/sci-biology/transfac-3.2-r1 new file mode 100644 index 000000000000..91dec5eae8be --- /dev/null +++ b/metadata/md5-cache/sci-biology/transfac-3.2-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install +DEPEND=emboss? ( sci-biology/emboss ) +DESCRIPTION=A database of eucaryotic transcription factors +EAPI=6 +HOMEPAGE=http://www.gene-regulation.com/pub/databases.html +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=3 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z +_md5_=d8fcea543b5af9fc877c63800e1bd6d3 diff --git a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 new file mode 100644 index 000000000000..c096695590e7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install prepare setup +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data +EAPI=4 +HOMEPAGE=http://www.tree-puzzle.de +IUSE=mpi +KEYWORDS=~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +RDEPEND=mpi? ( virtual/mpi ) +RESTRICT=test +SLOT=0 +SRC_URI=http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=6f933fde60eb23f0e50fbe5e137bbc7e diff --git a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 new file mode 100644 index 000000000000..119076c2f725 --- /dev/null +++ b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=prepare +DEPEND=x11-libs/wxGTK:3.0[X] >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=A phylogenetic tree viewer +EAPI=5 +HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/wxGTK:3.0[X] +SLOT=0 +SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf wxwidgets 04e063b0eff26daaea83d859dd9d6e05 +_md5_=ce129f3e61a849cfd3654e5a9fa4b17a diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r1 b/metadata/md5-cache/sci-biology/trf-4.04-r1 new file mode 100644 index 000000000000..3195b5c5feec --- /dev/null +++ b/metadata/md5-cache/sci-biology/trf-4.04-r1 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install unpack +DESCRIPTION=Tandem Repeats Finder +EAPI=6 +HOMEPAGE=http://tandem.bu.edu/trf/trf.html +KEYWORDS=amd64 x86 +LICENSE=trf +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=http://tandem.bu.edu/trf/downloads/trf404.linux +_md5_=51a51c14c6646aaa7d7494d561535729 diff --git a/metadata/md5-cache/sci-biology/trnascan-se-1.31 b/metadata/md5-cache/sci-biology/trnascan-se-1.31 new file mode 100644 index 000000000000..5a2f4fc6e741 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trnascan-se-1.31 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install prepare test +DESCRIPTION=tRNA detection in large-scale genome sequences +EAPI=6 +HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/ +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> trnascan-se-1.31.tar.gz +_eclasses_=multilib 97f470f374f2e94ccab04a2fb21d811e perl-functions 01e8c68d5a528bbcda4d3c60205983df toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=3f4bcdf31fe276f90a95e2f4b311deae diff --git a/metadata/md5-cache/sci-biology/uchime-4.2.40 b/metadata/md5-cache/sci-biology/uchime-4.2.40 new file mode 100644 index 000000000000..daffc0c3042f --- /dev/null +++ b/metadata/md5-cache/sci-biology/uchime-4.2.40 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install prepare test +DEPEND=sys-devel/make >=dev-util/cmake-3.9.6 +DESCRIPTION=Fast, accurate chimera detection +EAPI=6 +HOMEPAGE=http://www.drive5.com/uchime/ +IUSE=debug +KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +SLOT=0 +SRC_URI=http://drive5.com/uchime/uchime4.2.40_src.tar.gz +_eclasses_=cmake-utils 57384a259cf0c7985ce651b2c0865405 desktop 1b286a7e7143d8c4ec89cd0d2743a097 eapi7-ver d97a56a62c7df8614afddcb25f5ff00f epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e multiprocessing cac3169468f893670dac3e7cb940e045 ninja-utils d2e7e7d290428bb25c56dcf2502badc1 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils f2c8335407f0b935b0a96d4adf23ef25 +_md5_=6adcbb8c658bdc3c40f797c61f5c58b0 diff --git a/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 new file mode 100644 index 000000000000..2597f362c85e --- /dev/null +++ b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install postinst prepare prerm setup +DEPEND=app-arch/unzip !<sci-biology/ucsc-genome-browser-223 mysql? ( virtual/mysql ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 +DESCRIPTION=The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath +EAPI=5 +HOMEPAGE=http://genome.ucsc.edu/ +IUSE=+mysql +server static-libs vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=blat +RDEPEND=app-arch/unzip !<sci-biology/ucsc-genome-browser-223 mysql? ( virtual/mysql ) server? ( virtual/httpd-cgi ) >=app-admin/webapp-config-1.50.15 +REQUIRED_USE=server? ( mysql ) +SLOT=0 +SRC_URI=http://hgdownload.cse.ucsc.edu/admin/jksrc.v260.zip +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf webapp 6ae2395d7f341093c36057cb4f69101a +_md5_=e8bc8c4496d6c751b8f8452324e059f4 diff --git a/metadata/md5-cache/sci-biology/unafold-3.8-r1 b/metadata/md5-cache/sci-biology/unafold-3.8-r1 new file mode 100644 index 000000000000..e175b285bf25 --- /dev/null +++ b/metadata/md5-cache/sci-biology/unafold-3.8-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=prepare +DESCRIPTION=Unified Nucleic Acid Folding and hybridization package +EAPI=5 +HOMEPAGE=http://mfold.rna.albany.edu/ +IUSE=custom-cflags +KEYWORDS=~amd64 ~x86 +LICENSE=unafold +SLOT=0 +SRC_URI=http://dinamelt.bioinfo.rpi.edu/download/unafold-3.8.tar.bz2 +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=f6e357557efc2f86eab0adadd32142ce diff --git a/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 new file mode 100644 index 000000000000..3e9a8b5e2296 --- /dev/null +++ b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 @@ -0,0 +1,11 @@ +DEFINED_PHASES=install +DESCRIPTION=update_blastdb.pl for local blast db maintainance +EAPI=5 +HOMEPAGE=http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=dev-lang/perl !sci-biology/ncbi-tools++ +SLOT=0 +SRC_URI=ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/12_0_0/ncbi_cxx--12_0_0.tar.gz +_eclasses_=estack 43ddf5aaffa7a8d0482df54d25a66a1f versionator 26ca8a8bd95d6a74122c08ba98a4ee72 +_md5_=bc882208706b78e231cbfd78c7b5799e diff --git a/metadata/md5-cache/sci-biology/vaal-46233-r2 b/metadata/md5-cache/sci-biology/vaal-46233-r2 new file mode 100644 index 000000000000..fb9109c2d202 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vaal-46233-r2 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare +DEPEND=!sci-biology/allpaths !sci-biology/allpathslg dev-libs/boost >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Algorithm for detecting SNPs, indels, and other polymorphisms +EAPI=6 +HOMEPAGE=http://www.broadinstitute.org/science/programs/genome-biology/crd/ +IUSE=openmp +KEYWORDS=amd64 +LICENSE=Whitehead-MIT +RDEPEND=!sci-biology/allpaths !sci-biology/allpathslg +SLOT=0 +SRC_URI=ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/vaal-46233.tar.gz ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc https://dev.gentoo.org/~mgorny/dist/vaal-46233_remove-namespace-std.patch.bz2 +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 libtool 0081a71a261724730ec4c248494f044d multilib 97f470f374f2e94ccab04a2fb21d811e toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 +_md5_=7ca22b906d6f7e7c4fe2f2f35eedfb6b diff --git a/metadata/md5-cache/sci-biology/vcftools-0.1.14 b/metadata/md5-cache/sci-biology/vcftools-0.1.14 new file mode 100644 index 000000000000..3fcd202d89bb --- /dev/null +++ b/metadata/md5-cache/sci-biology/vcftools-0.1.14 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure prepare +DEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack ) virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DESCRIPTION=Tools for working with VCF (Variant Call Format) files +EAPI=6 +HOMEPAGE=http://vcftools.sourceforge.net/ +IUSE=lapack +KEYWORDS=~x86 ~amd64 +LICENSE=LGPL-3 +RDEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack ) +SLOT=0 +SRC_URI=https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz +_eclasses_=autotools d0e5375d47f4c809f406eb892e531513 desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 libtool 0081a71a261724730ec4c248494f044d ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e perl-functions 01e8c68d5a528bbcda4d3c60205983df preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=c40169dc993f3444a3e2f41ad69a920d diff --git a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 new file mode 100644 index 000000000000..b6c62a7e3240 --- /dev/null +++ b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install postinst prepare +DEPEND=sys-libs/zlib doc? ( virtual/latex-base ) +DESCRIPTION=A sequence assembler for very short reads +EAPI=4 +HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ +IUSE=-doc +KEYWORDS=amd64 x86 +LICENSE=GPL-2 +RDEPEND=sys-libs/zlib +SLOT=0 +SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.0.18.tgz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=81d9bd82f6f3df3f4b73fa7d65b5d95e diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10 new file mode 100644 index 000000000000..a7028a35342b --- /dev/null +++ b/metadata/md5-cache/sci-biology/velvet-1.2.10 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare test +DEPEND=doc? ( virtual/latex-base ) +DESCRIPTION=A sequence assembler for very short reads +EAPI=5 +HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ +IUSE=doc openmp +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz +_eclasses_=desktop 1b286a7e7143d8c4ec89cd0d2743a097 epatch 9a5f039771f143195164a15a4faa41a1 estack 43ddf5aaffa7a8d0482df54d25a66a1f eutils 5b8ce72259e08104b337fe28c6de5dbc flag-o-matic 5128c4729303400bd8d4b0b966530955 ltprune 607e058da37aa6dabfa408b7d61da72e multilib 97f470f374f2e94ccab04a2fb21d811e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 1e35303c63cd707f6c3422b4493d5607 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf +_md5_=420632435bf1efe77241192fff993a20 diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 new file mode 100644 index 000000000000..159cfd47df0b --- /dev/null +++ b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) python? ( dev-lang/swig:0 ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-lang/perl:=[-build(-)] +DESCRIPTION=RNA secondary structure prediction and comparison +EAPI=5 +HOMEPAGE=http://www.tbi.univie.ac.at/~ivo/RNA/ +IUSE=doc openmp python static-libs python_targets_python2_7 +KEYWORDS=amd64 ppc x86 +LICENSE=vienna-rna +RDEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) dev-lang/perl:=[-build(-)] +REQUIRED_USE=python? 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