reinit the tree, so we can have metadata

author: V3n3RiX <venerix@redcorelinux.org> 2017-10-09 18:53:29 +0100
committer: V3n3RiX <venerix@redcorelinux.org> 2017-10-09 18:53:29 +0100
commit: 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch)
tree: ba5f07bf3f9d22d82e54a462313f5d244036c768 /metadata/md5-cache/sci-biology
198 files changed, 2412 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..e86c2abbb5b1
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..ee83ee8a9df0
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70	webapp	a76ebd3cb5649737496e8238992dd7ca
+_md5_=bccaeef3292f6df307fc14fb5a2a74b2
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..225fb56fb9a6
--- /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=http://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_=416040c81e5246e2fd1669dcb03c9a3d
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..d0911d7f0ba0
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=3b173739bd4e2f9d61a49918b3b8bc05
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..69948cd04d54
--- /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-1.15:1.15 ) >=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
+_eclasses_=autotools	dc412f38566b91012efd58b9c203e6c3	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=89ad1ab9497c178e43302814589f5f26
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..4c0634652876
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	java-ant-2	4e2b30d918dda38a51839a4d45282b62	java-pkg-opt-2	77d2e22d0de7640f817d20e861c0ff3f	java-utils-2	1971a6927fcd7ec839f7e12b28a24bdd	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=6bd792e8b76c06ee993b88f83e48b907
diff --git a/metadata/md5-cache/sci-biology/amos-3.1.0-r3 b/metadata/md5-cache/sci-biology/amos-3.1.0-r3
new file mode 100644
index 000000000000..0984d1ca68a3
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/amos-3.1.0-r3
@@ -0,0 +1,14 @@
+DEFINED_PHASES=install prepare setup
+DEPEND=qt4? ( dev-qt/qtcore:4 ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=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=qt4 python_targets_python2_7
+KEYWORDS=~amd64 ~x86
+LICENSE=Artistic
+RDEPEND=qt4? ( dev-qt/qtcore:4 ) 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_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	dc412f38566b91012efd58b9c203e6c3	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	python-single-r1	317a2557b4d7319a7418225f65accf77	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=df778f6981c64e06ab2354697c3fc4a6
diff --git a/metadata/md5-cache/sci-biology/arb-5.1-r1 b/metadata/md5-cache/sci-biology/arb-5.1-r1
new file mode 100644
index 000000000000..c44c07cca1d6
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/arb-5.1-r1
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile install prepare 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 ) ) )
+DESCRIPTION=Tools for DNA/RNA sequence database handling and phylogenetic analysis
+EAPI=2
+HOMEPAGE=http://www.arb-home.de/
+IUSE=+opengl
+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
+SLOT=0
+SRC_URI=http://download.arb-home.de/release/arb_5.1/arbsrc.tgz -> arb-5.1.tgz mirror://gentoo/arb-5.1-glibc2.10.patch.bz2 https://dev.gentoo.org/~jlec/arb-5.1-linker.patch.bz2
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=55cafcf3d37a81cfa2273ca02c35bb00
diff --git a/metadata/md5-cache/sci-biology/arb-5.2 b/metadata/md5-cache/sci-biology/arb-5.2
new file mode 100644
index 000000000000..8a2d215e3afb
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/arb-5.2
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile install prepare 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
+DESCRIPTION=Tools for DNA/RNA sequence database handling and phylogenetic analysis
+EAPI=4
+HOMEPAGE=http://www.arb-home.de/
+IUSE=+opengl
+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
+SLOT=0
+SRC_URI=http://download.arb-home.de/release/arb_5.2/arbsrc.tgz -> arb-5.2.tgz https://dev.gentoo.org/~jlec/distfiles/arb-5.2-linker.patch.bz2
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=f0ab0e2c5ca080655274968b7915db12
diff --git a/metadata/md5-cache/sci-biology/arb-5.3 b/metadata/md5-cache/sci-biology/arb-5.3
new file mode 100644
index 000000000000..718eca60b523
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/arb-5.3
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile install prepare 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
+DESCRIPTION=Tools for DNA/RNA sequence database handling and phylogenetic analysis
+EAPI=4
+HOMEPAGE=http://www.arb-home.de/
+IUSE=+opengl
+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
+SLOT=0
+SRC_URI=http://download.arb-home.de/release/arb_5.3/arbsrc.tgz -> arb-5.3.tgz https://dev.gentoo.org/~jlec/distfiles/arb-5.3-linker.patch.xz
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=bf2908058bcd4bfbaa7c0eb481d7c999
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..41304cabd1e3
--- /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	185a06792159ca143528e7010368e8af
+_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..556b1ae883b5
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=5660f556708e8c3b5d43c9ef832e66ec
diff --git a/metadata/md5-cache/sci-biology/bamtools-2.4.1 b/metadata/md5-cache/sci-biology/bamtools-2.4.1
new file mode 100644
index 000000000000..922cda27556d
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/bamtools-2.4.1
@@ -0,0 +1,12 @@
+DEFINED_PHASES=compile configure install prepare test
+DEPEND=>=dev-libs/jsoncpp-1.8.0 sys-libs/zlib sys-devel/make >=dev-util/cmake-3.7.2
+DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files
+EAPI=6
+HOMEPAGE=https://github.com/pezmaster31/bamtools
+KEYWORDS=~amd64 ~x86
+LICENSE=MIT
+RDEPEND=>=dev-libs/jsoncpp-1.8.0 sys-libs/zlib
+SLOT=0
+SRC_URI=https://github.com/pezmaster31/bamtools/archive/v2.4.1.tar.gz -> bamtools-2.4.1.tar.gz
+_eclasses_=cmake-utils	f9fb12e2dbe2e0c9c17f030bae85eb02	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	ninja-utils	ebb2eaddc6331c4fa000b8eb8f6fe074	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=d1565aa3d9a639f7316a0c8588ecfc41
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..79a9f03753a6
--- /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	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=e289371e3fec376baf8fe36c652ca521
diff --git a/metadata/md5-cache/sci-biology/beast-mcmc-1.7.5-r1 b/metadata/md5-cache/sci-biology/beast-mcmc-1.7.5-r1
new file mode 100644
index 000000000000..8ac98d5e6f87
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/beast-mcmc-1.7.5-r1
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile configure install preinst prepare setup test
+DEPEND=>=virtual/jdk-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2
+DESCRIPTION=Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences
+EAPI=5
+HOMEPAGE=https://github.com/beast-dev/beast-mcmc
+IUSE=elibc_FreeBSD elibc_FreeBSD
+KEYWORDS=~amd64 ~x86
+LICENSE=LGPL-3
+RDEPEND=>=virtual/jre-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0-r3
+SLOT=0
+SRC_URI=https://dev.gentoo.org/~jlec/distfiles/beast-mcmc-1.7.5.tar.xz
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	java-ant-2	4e2b30d918dda38a51839a4d45282b62	java-pkg-2	c4e6af2574fd1dc79b43a6e27af4b5fb	java-utils-2	1971a6927fcd7ec839f7e12b28a24bdd	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=ff6d5ad394902a1137f7b3a310e2da17
diff --git a/metadata/md5-cache/sci-biology/beast-mcmc-9999 b/metadata/md5-cache/sci-biology/beast-mcmc-9999
new file mode 100644
index 000000000000..b26937a98b42
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/beast-mcmc-9999
@@ -0,0 +1,11 @@
+DEFINED_PHASES=compile configure install preinst prepare setup test unpack
+DEPEND=>=virtual/jdk-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2 || ( dev-vcs/subversion[http] dev-vcs/subversion[webdav-neon] dev-vcs/subversion[webdav-serf] ) net-misc/rsync
+DESCRIPTION=Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences
+EAPI=2
+HOMEPAGE=https://github.com/beast-dev/beast-mcmc
+IUSE=elibc_FreeBSD elibc_FreeBSD
+LICENSE=LGPL-3
+RDEPEND=>=virtual/jre-1.5 dev-java/colt:0 dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 dev-java/matrix-toolkits-java dev-java/commons-math:2 dev-java/jdom-jaxen:1.0 >=dev-java/java-config-2.2.0-r3
+SLOT=0
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	java-ant-2	4e2b30d918dda38a51839a4d45282b62	java-pkg-2	c4e6af2574fd1dc79b43a6e27af4b5fb	java-utils-2	1971a6927fcd7ec839f7e12b28a24bdd	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	subversion	a5d5826a85609611f098c0553eb24cc1	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=8ad11964919894b7a04467aea903b1c3
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..d55847e96e3a
--- /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:3.5 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
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	python-any-r1	27d7f9da7187d283b7f3eae8390b7b09	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=76f5a1f39ff7b393994b8a22dc4a192f
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..00cc3c43a82d
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	autotools-utils	5a4611dfba155b1659528663fad4cd5e	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..1a8e5efc8cba
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=9731727dae2a2514bcaa486b0059272e
diff --git a/metadata/md5-cache/sci-biology/biopandas-0.1.4 b/metadata/md5-cache/sci-biology/biopandas-0.1.4
new file mode 100644
index 000000000000..c9eb07ef6313
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/biopandas-0.1.4
@@ -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_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] test? ( dev-python/nose[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_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 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)]
+DESCRIPTION=Molecular Structures in Pandas DataFrames
+EAPI=5
+HOMEPAGE=https://rasbt.github.io/biopandas/ https://github.com/rasbt/biopandas https://pypi.python.org/pypi/BioPandas
+IUSE=test python_targets_python2_7 python_targets_python3_4 python_targets_python3_5
+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_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] dev-python/pandas[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)] sci-libs/scipy[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_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 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-)]
+REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_4 python_targets_python3_5 )
+SLOT=0
+SRC_URI=mirror://pypi/B/BioPandas/biopandas-0.1.4.tar.gz
+_eclasses_=distutils-r1	372bbe39047c0a2550319a3a82f3e063	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multibuild	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	xdg-utils	f2c8335407f0b935b0a96d4adf23ef25
+_md5_=4bf8773b4c6c512c3e616bf999994904
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..e9a8b94bbdd0
--- /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.python.org/pypi/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	372bbe39047c0a2550319a3a82f3e063	multibuild	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	xdg-utils	f2c8335407f0b935b0a96d4adf23ef25
+_md5_=50d773beb88c02a8cbddc153bb75a0e6
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..f4cfa897bcca
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..4b3525b25e64
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	git-2	195a672bfaf52d868442171c9469bbb6	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..a9290a159eb9
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..204c8a3ebc72
--- /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	6f5991c7101863d0b29df63990ad852e	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..f5e6e8de7993
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	git-2	195a672bfaf52d868442171c9469bbb6	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..00553d57b165
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..ba26bf2d5401
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	git-2	195a672bfaf52d868442171c9469bbb6	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..1c8895b23bda
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..076f25d9f091
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	git-2	195a672bfaf52d868442171c9469bbb6	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70
+_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..53a57ff3bbec
--- /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.python.org/pypi/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_=distutils-r1	372bbe39047c0a2550319a3a82f3e063	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multibuild	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	xdg-utils	f2c8335407f0b935b0a96d4adf23ef25
+_md5_=4a82fa47ce713f463d26f604da0ee94a
diff --git a/metadata/md5-cache/sci-biology/bioruby-1.4.3.0001-r1 b/metadata/md5-cache/sci-biology/bioruby-1.4.3.0001-r1
new file mode 100644
index 000000000000..6a8b72ae7cb9
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/bioruby-1.4.3.0001-r1
@@ -0,0 +1,14 @@
+DEFINED_PHASES=compile configure install prepare setup test unpack
+DEPEND=test? ( ruby_targets_ruby22? ( dev-ruby/libxml[ruby_targets_ruby22] ) ) ruby_targets_ruby22? ( dev-lang/ruby:2.2 ) ruby_targets_ruby22? ( doc? ( dev-ruby/rake[ruby_targets_ruby22] ) ) ruby_targets_ruby22? ( test? ( dev-ruby/rake[ruby_targets_ruby22] ) ) ruby_targets_ruby22? ( virtual/rubygems[ruby_targets_ruby22] ) test? ( ruby_targets_ruby22? ( virtual/rubygems[ruby_targets_ruby22] ) )
+DESCRIPTION=An integrated environment for bioinformatics using the Ruby language
+EAPI=5
+HOMEPAGE=http://bioruby.org/
+IUSE=test elibc_FreeBSD ruby_targets_ruby22 doc test test
+KEYWORDS=amd64 ~ppc x86
+LICENSE=Ruby
+RDEPEND=ruby_targets_ruby22? ( dev-ruby/libxml[ruby_targets_ruby22] ) ruby_targets_ruby22? ( dev-lang/ruby:2.2 ) ruby_targets_ruby22? ( virtual/rubygems[ruby_targets_ruby22] )
+REQUIRED_USE=|| ( ruby_targets_ruby22 )
+SLOT=0
+SRC_URI=http://bioruby.org/archive/bioruby-1.4.3.0001.tar.gz
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	java-utils-2	1971a6927fcd7ec839f7e12b28a24bdd	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	ruby-fakegem	bafb56b9a7b7e84fd091508783628e78	ruby-ng	dbd648644c9f5bec523dc17dc34d8671	ruby-utils	453e0fe0dd06baac93b584c91528cc62	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=0bff0c3e2db3a9967274e417280ca082
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..db3ef62c6ae7
--- /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_ruby22? ( dev-ruby/libxml[ruby_targets_ruby22] ) ruby_targets_ruby23? ( dev-ruby/libxml[ruby_targets_ruby23] ) ) ruby_targets_ruby22? ( dev-lang/ruby:2.2 ) ruby_targets_ruby23? ( dev-lang/ruby:2.3 ) ruby_targets_ruby22? ( doc? ( dev-ruby/rake[ruby_targets_ruby22] ) ) ruby_targets_ruby23? ( doc? ( dev-ruby/rake[ruby_targets_ruby23] ) ) ruby_targets_ruby22? ( test? ( dev-ruby/rake[ruby_targets_ruby22] ) ) ruby_targets_ruby23? ( test? ( dev-ruby/rake[ruby_targets_ruby23] ) ) ruby_targets_ruby22? ( virtual/rubygems[ruby_targets_ruby22] ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) test? ( ruby_targets_ruby22? ( virtual/rubygems[ruby_targets_ruby22] ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] ) )
+DESCRIPTION=An integrated environment for bioinformatics using the Ruby language
+EAPI=6
+HOMEPAGE=http://bioruby.org/
+IUSE=test elibc_FreeBSD ruby_targets_ruby22 ruby_targets_ruby23 doc test test
+KEYWORDS=~amd64 ~ppc ~x86
+LICENSE=Ruby
+RDEPEND=ruby_targets_ruby22? ( dev-ruby/libxml[ruby_targets_ruby22] ) ruby_targets_ruby23? ( dev-ruby/libxml[ruby_targets_ruby23] ) ruby_targets_ruby22? ( dev-lang/ruby:2.2 ) ruby_targets_ruby23? ( dev-lang/ruby:2.3 ) ruby_targets_ruby22? ( virtual/rubygems[ruby_targets_ruby22] ) ruby_targets_ruby23? ( virtual/rubygems[ruby_targets_ruby23] )
+REQUIRED_USE=|| ( ruby_targets_ruby22 ruby_targets_ruby23 )
+SLOT=0
+SRC_URI=mirror://rubygems/bio-1.5.1.gem
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	java-utils-2	1971a6927fcd7ec839f7e12b28a24bdd	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	ruby-fakegem	bafb56b9a7b7e84fd091508783628e78	ruby-ng	dbd648644c9f5bec523dc17dc34d8671	ruby-utils	453e0fe0dd06baac93b584c91528cc62	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=279e084b7a2a210af63381996d8b6488
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..cd8118f0ed80
--- /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	185a06792159ca143528e7010368e8af
+_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..2568b5d69fe0
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=2fe1853c7621b633d2ee794ef3176e3f
diff --git a/metadata/md5-cache/sci-biology/bowtie-1.1.2 b/metadata/md5-cache/sci-biology/bowtie-1.1.2
new file mode 100644
index 000000000000..d652aea16e3e
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/bowtie-1.1.2
@@ -0,0 +1,12 @@
+DEFINED_PHASES=compile install prepare
+DEPEND=app-arch/unzip tbb? ( dev-cpp/tbb )
+DESCRIPTION=Popular short read aligner for Next-generation sequencing data
+EAPI=5
+HOMEPAGE=http://bowtie-bio.sourceforge.net/
+IUSE=examples +tbb
+KEYWORDS=amd64 x86 ~x64-macos
+LICENSE=Artistic
+SLOT=1
+SRC_URI=mirror://sourceforge/bowtie-bio/bowtie-1.1.2-src.zip
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=d123eea345ef4aa6c2c174df53575eeb
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..155d396e3ec4
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=069dc133bc01cabadeda1e327034b7a7
diff --git a/metadata/md5-cache/sci-biology/bowtie-2.2.6 b/metadata/md5-cache/sci-biology/bowtie-2.2.6
new file mode 100644
index 000000000000..edee1f172dc2
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/bowtie-2.2.6
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile install pretend
+DEPEND=dev-lang/perl app-arch/unzip tbb? ( dev-cpp/tbb )
+DESCRIPTION=Popular short read aligner for Next-generation sequencing data
+EAPI=5
+HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/
+IUSE=examples cpu_flags_x86_sse2 +tbb
+KEYWORDS=amd64 x86
+LICENSE=GPL-3
+RDEPEND=dev-lang/perl
+SLOT=2
+SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.2.6/bowtie2-2.2.6-source.zip
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=9a4ea0d94d151da708192284a1117dd7
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..b2feff8ad4f2
--- /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	185a06792159ca143528e7010368e8af
+_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..489a9b824641
--- /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	185a06792159ca143528e7010368e8af
+_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..c87c92af1291
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..c98c75166223
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..63df23d16873
--- /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	185a06792159ca143528e7010368e8af
+_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..9842125c00cd
--- /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
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new file mode 100644
index 000000000000..9d932f7e78d4
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/clustalx-2.1-r1
@@ -0,0 +1,12 @@
+DEFINED_PHASES=compile configure install prepare unpack
+DEPEND=dev-qt/qtcore:4 dev-qt/qtgui:4
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+EAPI=5
+HOMEPAGE=http://www.ebi.ac.uk/tools/clustalw2/
+KEYWORDS=amd64 x86
+LICENSE=GPL-3 LGPL-3
+RDEPEND=dev-qt/qtcore:4 dev-qt/qtgui:4 >=sci-biology/clustalw-2.1
+SLOT=0
+SRC_URI=http://www.clustal.org/download/current/clustalx-2.1.tar.gz
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new file mode 100644
index 000000000000..7cd8633bd4c0
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/clustalx-2.1-r2
@@ -0,0 +1,12 @@
+DEFINED_PHASES=configure install prepare
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+HOMEPAGE=http://www.ebi.ac.uk/tools/clustalw2/
+KEYWORDS=~amd64 ~x86
+LICENSE=GPL-3 LGPL-3
+RDEPEND=dev-qt/qtcore:4 dev-qt/qtgui:4 >=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
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new file mode 100644
index 000000000000..5c4e6170ffda
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+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
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+SRC_URI=consed-29-sources.tar.gz consed-29-linux.tar.gz
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index 000000000000..603d7de9f726
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+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_python2_7(+)] dev-cpp/eigen:3 virtual/pkgconfig >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=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_python2_7(+)]
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new file mode 100644
index 000000000000..60c35396bc6a
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/cutg-160-r1
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+DEPEND=emboss? ( sci-biology/emboss )
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+HOMEPAGE=http://www.kazusa.or.jp/codon/
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+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
+LICENSE=public-domain
+RDEPEND=emboss? ( sci-biology/emboss )
+RESTRICT=binchecks strip
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index 000000000000..af17f98104c5
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@@ -0,0 +1,10 @@
+DEFINED_PHASES=compile install postinst prepare
+DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment
+EAPI=5
+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
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index 000000000000..e83238c60dbb
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+DEFINED_PHASES=compile install
+DESCRIPTION=Multiple sequence alignment
+EAPI=5
+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
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index 000000000000..e84d5a357059
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+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
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+EAPI=6
+HOMEPAGE=http://cbcb.umd.edu/software/ELPH/
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos
+LICENSE=Artistic
+SLOT=0
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index 000000000000..d501a327e417
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+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
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index 000000000000..7820052b3b54
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index 000000000000..4c74a56235e0
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+SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.660.tar.gz -> embassy-domalign-0.1.660.tar.gz
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index 000000000000..4149b8ee4296
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+HOMEPAGE=http://emboss.sourceforge.net/
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+SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.660.tar.gz -> embassy-domsearch-0.1.660.tar.gz
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+DESCRIPTION=EMBOSS integrated version of Simple menu of EMBOSS applications
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+HOMEPAGE=http://emboss.sourceforge.net/
+IUSE=ncurses mysql pdf png postgres static-libs X
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+SLOT=0
+SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.660.tar.gz -> embassy-emnu-1.05.660.tar.gz
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+HOMEPAGE=http://emboss.sourceforge.net/
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+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
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+HOMEPAGE=http://emboss.sourceforge.net/
+IUSE=mysql pdf png postgres static-libs X
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+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
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+EAPI=6
+HOMEPAGE=http://emboss.sourceforge.net/
+IUSE=mysql pdf png postgres static-libs X
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+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
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+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
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+SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.660.tar.gz -> embassy-meme-4.7.660.tar.gz
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+SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.660.tar.gz -> embassy-mse-3.0.0.660.tar.gz
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index 000000000000..bc39cbf990f6
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+SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.660.tar.gz -> embassy-structure-0.1.660.tar.gz
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+HOMEPAGE=http://emboss.sourceforge.net/
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+DESCRIPTION=The European Molecular Biology Open Software Suite - A sequence analysis package
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+HOMEPAGE=http://eugene.toulouse.inra.fr/
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+RDEPEND=media-libs/gd[png] media-libs/libpng:0=
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+RDEPEND=dev-libs/glib:2
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+KEYWORDS=~amd64 ~x86
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new file mode 100644
index 000000000000..7669e32e77d0
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/fasttree-2.1.8
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile configure install prepare test unpack
+DEPEND=sys-devel/make >=dev-util/cmake-3.7.2
+DESCRIPTION=Fast inference of approximately-maximum-likelihood phylogenetic trees
+EAPI=5
+HOMEPAGE=http://www.microbesonline.org/fasttree/
+IUSE=double-precision openmp cpu_flags_x86_sse3
+KEYWORDS=~amd64 ~x86
+LICENSE=GPL-2
+REQUIRED_USE=?? ( double-precision cpu_flags_x86_sse3 )
+SLOT=0
+SRC_URI=http://www.microbesonline.org/fasttree/FastTree-2.1.8.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.8.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.8.tar.gz
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new file mode 100644
index 000000000000..dd4a6f663f72
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r2
@@ -0,0 +1,9 @@
+DEFINED_PHASES=install
+DESCRIPTION=Graphical viewer for chromatogram files
+EAPI=5
+HOMEPAGE=http://www.geospiza.com/finchtv/
+KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux
+LICENSE=finchtv
+SLOT=0
+SRC_URI=http://www.geospiza.com/finchtv/download/programs/linux/finchtv_1_3_1.tar.gz
+_md5_=ae49772a5dce24695f0ae65993bae0c1
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new file mode 100644
index 000000000000..a9310a08b956
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r3
@@ -0,0 +1,10 @@
+DEFINED_PHASES=install
+DESCRIPTION=Graphical viewer for chromatogram files
+EAPI=6
+HOMEPAGE=http://www.geospiza.com/finchtv/
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
+LICENSE=finchtv
+SLOT=0
+SRC_URI=http://www.geospiza.com/finchtv/download/programs/linux/finchtv_1_3_1.tar.gz
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new file mode 100644
index 000000000000..7f34af898ac5
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/foldingathome-7.4.4-r2
@@ -0,0 +1,13 @@
+DEFINED_PHASES=config install postinst postrm setup
+DEPEND=virtual/pkgconfig
+DESCRIPTION=Folding@Home is a distributed computing project for protein folding
+EAPI=6
+HOMEPAGE=http://folding.stanford.edu/FAQ-SMP.html
+KEYWORDS=~amd64 ~x86
+LICENSE=FAH-EULA-2014 FAH-special-permission
+RDEPEND=app-arch/bzip2 sys-devel/gcc sys-libs/glibc sys-libs/zlib
+RESTRICT=mirror bindist strip
+SLOT=0
+SRC_URI=x86? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.5-32bit/v7.4/fahclient_7.4.4-32bit-release.tar.bz2 ) amd64? ( https://fah.stanford.edu/file-releases/public/release/fahclient/centos-5.3-64bit/v7.4/fahclient_7.4.4-64bit-release.tar.bz2 )
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new file mode 100644
index 000000000000..cb0429446e59
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/gatk-2.4
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile configure install preinst prepare setup unpack
+DEPEND=>=virtual/jdk-1.6 >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2
+DESCRIPTION=The Genome Analysis Toolkit
+EAPI=5
+HOMEPAGE=http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
+IUSE=elibc_FreeBSD elibc_FreeBSD
+KEYWORDS=~amd64
+LICENSE=MIT
+RDEPEND=>=virtual/jre-1.6 >=dev-java/java-config-2.2.0-r3
+SLOT=0
+SRC_URI=https://github.com/broadgsa/gatk/archive/2.4.tar.gz -> gatk-2.4.tar.gz
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new file mode 100644
index 000000000000..a977d44c92a3
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/gatk-9999
@@ -0,0 +1,11 @@
+DEFINED_PHASES=compile configure install preinst prepare setup unpack
+DEPEND=>=virtual/jdk-1.6 dev-vcs/git dev-vcs/git >=dev-java/java-config-2.2.0-r3 >=dev-java/ant-core-1.8.2:0 >=dev-java/javatoolkit-0.3.0-r2
+DESCRIPTION=The Genome Analysis Toolkit
+EAPI=5
+HOMEPAGE=http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
+IUSE=elibc_FreeBSD elibc_FreeBSD
+LICENSE=MIT
+RDEPEND=>=virtual/jre-1.6 >=dev-java/java-config-2.2.0-r3
+SLOT=0
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new file mode 100644
index 000000000000..c05a5c2579e6
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/gibbs-3.1
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+DEFINED_PHASES=compile configure install postinst prepare test
+DEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4
+DESCRIPTION=Identify motifs, conserved regions, in DNA or protein sequences
+EAPI=4
+HOMEPAGE=http://bayesweb.wadsworth.org/gibbs/gibbs.html
+IUSE=mpi
+KEYWORDS=amd64 x86
+LICENSE=GPL-2
+RDEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 )
+SLOT=0
+SRC_URI=mirror://gentoo/gibbs-3.1.tar.gz
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+_md5_=e28918ff8ca46c8b8254e4e36f8d0bcf
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new file mode 100644
index 000000000000..d74704924190
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/glimmer-3.02-r3
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+DEFINED_PHASES=compile install prepare
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+HOMEPAGE=http://www.cbcb.umd.edu/software/glimmer/
+KEYWORDS=amd64 x86
+LICENSE=Artistic
+RDEPEND=app-shells/tcsh
+SLOT=0
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index 000000000000..8ecbaec294b2
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+++ b/metadata/md5-cache/sci-biology/glimmer-3.02b
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+EAPI=5
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+KEYWORDS=~amd64 ~x86
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+RDEPEND=app-shells/tcsh sci-biology/elph
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index 000000000000..a09eb9691b99
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+KEYWORDS=amd64 x86
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+SLOT=0
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index 000000000000..9ea6427bde5b
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index 000000000000..0e4cb317c39c
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+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
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index 000000000000..7a94abaa4d02
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new file mode 100644
index 000000000000..604042875d81
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+DESCRIPTION=A DNA sequencing data management framework - C/C++ API
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index 000000000000..cd7a217f9861
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index 000000000000..1fa642f352dc
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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..d4f019b90099
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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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..a465d0bd0620
--- /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_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-1.15:1.15 ) >=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_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	dc412f38566b91012efd58b9c203e6c3	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	python-single-r1	317a2557b4d7319a7418225f65accf77	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
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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..a3eecbec084f
--- /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-1.15:1.15 ) >=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	dc412f38566b91012efd58b9c203e6c3	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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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..da8b41be0150
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af	vcs-snapshot	03289f51c769cf409d200d2d628cdd6e
+_md5_=e8bd620c581af022566733e65d479626
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..b298b5abeb67
--- /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=http://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=http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	fortran-2	9e7f20c99213f0627ff7f873d4aaa25d	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=abcc03749068210ba5c44ba0b4a85e27
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..fa670c1248d4
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..2bf7583b7964
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..ad783497f6dd
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..12581639213a
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..f1f4688e0d20
--- /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=http://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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	prefix	7b6fb2fc216b101b5d97d171925a847c	toolchain-funcs	185a06792159ca143528e7010368e8af
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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..c5de23202d44
--- /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	185a06792159ca143528e7010368e8af
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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..a4bf5df07230
--- /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	185a06792159ca143528e7010368e8af
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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..a05e09bb045e
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
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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..1017e2f127b8
--- /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
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diff --git a/metadata/md5-cache/sci-biology/phred-071220-r1 b/metadata/md5-cache/sci-biology/phred-071220-r1
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index 000000000000..bccbb696d5f6
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/phred-071220-r1
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+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
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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..00828abf5b15
--- /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-proto/xproto
+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	185a06792159ca143528e7010368e8af
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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..719db9077a6e
--- /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-proto/xproto
+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	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r3 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r3
new file mode 100644
index 000000000000..5eaecff6461a
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/phyml-2.4.5-r3
@@ -0,0 +1,10 @@
+DEFINED_PHASES=install prepare
+DESCRIPTION=Estimation of large phylogenies by maximum likelihood
+EAPI=6
+HOMEPAGE=http://atgc.lirmm.fr/phyml/
+KEYWORDS=amd64 ppc x86
+LICENSE=GPL-2
+SLOT=0
+SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz
+_eclasses_=multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/picard-1.103 b/metadata/md5-cache/sci-biology/picard-1.103
new file mode 100644
index 000000000000..e0cd3d8f4135
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/picard-1.103
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile configure install preinst prepare setup test
+DEPEND=>=virtual/jdk-1.6 dev-java/ant-apache-bcel:0 test? ( dev-java/testng:0 dev-lang/R ) dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0-r3 source? ( app-arch/zip ) >=dev-java/ant-core-1.8.2:0 dev-java/ant-apache-bcel dev-java/testng:0 dev-java/ant-junit4 >=dev-java/javatoolkit-0.3.0-r2
+DESCRIPTION=Java-based command-line utilities that manipulate SAM files
+EAPI=5
+HOMEPAGE=http://picard.sourceforge.net/
+IUSE=elibc_FreeBSD doc source test elibc_FreeBSD
+KEYWORDS=~amd64 ~x86
+LICENSE=Apache-2.0
+RDEPEND=>=virtual/jre-1.6 dev-java/snappy:1.0 dev-java/cofoja:0 dev-java/commons-jexl:2 dev-java/ant-core:0 >=dev-java/java-config-2.2.0-r3 source? ( app-arch/zip )
+SLOT=0
+SRC_URI=https://dev.gentoo.org/~ercpe/distfiles/sci-biology/picard/picard-1.103.tar.bz2
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	java-ant-2	4e2b30d918dda38a51839a4d45282b62	java-pkg-2	c4e6af2574fd1dc79b43a6e27af4b5fb	java-utils-2	1971a6927fcd7ec839f7e12b28a24bdd	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
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new file mode 100644
index 000000000000..6722c4e34e06
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/piler-1.0-r1
@@ -0,0 +1,11 @@
+DEFINED_PHASES=configure install
+DESCRIPTION=Analysis of repetitive DNA found in genome sequences
+EAPI=6
+HOMEPAGE=http://www.drive5.com/piler/
+KEYWORDS=amd64 x86
+LICENSE=public-domain
+RDEPEND=|| ( sci-biology/muscle sci-libs/libmuscle ) sci-biology/pals
+SLOT=0
+SRC_URI=http://www.drive5.com/piler/piler_source.tar.gz -> piler-1.0.tar.gz
+_eclasses_=multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r1 b/metadata/md5-cache/sci-biology/pilercr-1.0-r1
new file mode 100644
index 000000000000..8e8efc9ad948
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/pilercr-1.0-r1
@@ -0,0 +1,10 @@
+DEFINED_PHASES=configure install
+DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
+EAPI=6
+HOMEPAGE=http://www.drive5.com/pilercr/
+KEYWORDS=amd64 x86
+LICENSE=public-domain
+SLOT=0
+SRC_URI=http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> pilercr-1.0.tar.gz
+_eclasses_=multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/plink-1.07-r1 b/metadata/md5-cache/sci-biology/plink-1.07-r1
new file mode 100644
index 000000000000..c5ae9fdd9905
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/plink-1.07-r1
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile install prepare
+DEPEND=app-arch/unzip lapack? ( 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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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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..697535fab41c
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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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..4ec1401d1e30
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..63be9e96b258
--- /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	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.5 b/metadata/md5-cache/sci-biology/primer3-2.3.5
new file mode 100644
index 000000000000..9de4d843001f
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/primer3-2.3.5
@@ -0,0 +1,11 @@
+DEFINED_PHASES=compile install prepare test
+DEPEND=dev-lang/perl
+DESCRIPTION=Primer Design for PCR reactions
+EAPI=5
+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/primer3/2.3.5/primer3-2.3.5.tar.gz
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.6 b/metadata/md5-cache/sci-biology/primer3-2.3.6
new file mode 100644
index 000000000000..9b26f6c19de3
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/primer3-2.3.6
@@ -0,0 +1,11 @@
+DEFINED_PHASES=compile install prepare test
+DEPEND=dev-lang/perl
+DESCRIPTION=Primer Design for PCR reactions
+EAPI=5
+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/primer3/2.3.6/primer3-src-2.3.6.tar.gz
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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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..21f001a52b5e
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/primer3-2.3.7
@@ -0,0 +1,11 @@
+DEFINED_PHASES=compile install prepare test
+DEPEND=dev-lang/perl
+DESCRIPTION=Primer Design for PCR reactions
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+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
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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 @@
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+DEPEND=emboss? ( sci-biology/emboss )
+DESCRIPTION=A protein motif fingerprint database
+EAPI=6
+HOMEPAGE=http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
+IUSE=emboss minimal
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
+LICENSE=public-domain
+RDEPEND=emboss? ( sci-biology/emboss )
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diff --git a/metadata/md5-cache/sci-biology/probcons-1.12-r1 b/metadata/md5-cache/sci-biology/probcons-1.12-r1
new file mode 100644
index 000000000000..ebd290cabfbe
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/probcons-1.12-r1
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+DEFINED_PHASES=compile install postinst prepare
+DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
+EAPI=5
+HOMEPAGE=http://probcons.stanford.edu/
+KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux
+LICENSE=public-domain
+RDEPEND=!sci-geosciences/gmt sci-visualization/gnuplot
+SLOT=0
+SRC_URI=http://probcons.stanford.edu/probcons_v1_12.tar.gz
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new file mode 100644
index 000000000000..e5155ee6a1e3
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/prodigal-2.6.3
@@ -0,0 +1,10 @@
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+DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm
+EAPI=6
+HOMEPAGE=http://prodigal.ornl.gov/
+KEYWORDS=~amd64
+LICENSE=GPL-3
+SLOT=0
+SRC_URI=https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz -> prodigal-2.6.3.tar.gz
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diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.39 b/metadata/md5-cache/sci-biology/profphd-1.0.39
new file mode 100644
index 000000000000..c21de18f4ac4
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/profphd-1.0.39
@@ -0,0 +1,12 @@
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+DEPEND=dev-lang/perl
+DESCRIPTION=Secondary structure and solvent accessibility predictor
+EAPI=5
+HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
+LICENSE=GPL-2
+RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils
+SLOT=0
+SRC_URI=ftp://rostlab.org/profphd/profphd-1.0.39.tar.xz
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diff --git a/metadata/md5-cache/sci-biology/profphd-1.0.40 b/metadata/md5-cache/sci-biology/profphd-1.0.40
new file mode 100644
index 000000000000..11eba6beea24
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/profphd-1.0.40
@@ -0,0 +1,12 @@
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+HOMEPAGE=https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
+LICENSE=GPL-2
+RDEPEND=dev-lang/perl dev-perl/librg-utils-perl sci-libs/profnet sci-libs/profphd-utils
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diff --git a/metadata/md5-cache/sci-biology/prosite-2017.02 b/metadata/md5-cache/sci-biology/prosite-2017.02
new file mode 100644
index 000000000000..628597305894
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/prosite-2017.02
@@ -0,0 +1,12 @@
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+DEPEND=emboss? ( sci-biology/emboss )
+DESCRIPTION=A protein families and domains database
+EAPI=6
+HOMEPAGE=http://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_=390ff0ea61f44c9ea889684cad12b2b2
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..6ccf97068495
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	prefix	7b6fb2fc216b101b5d97d171925a847c	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_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..266f7b31187e
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	prefix	7b6fb2fc216b101b5d97d171925a847c	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_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..cfdd30b8ef95
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	prefix	7b6fb2fc216b101b5d97d171925a847c	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_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..c68c8738c9c5
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	prefix	7b6fb2fc216b101b5d97d171925a847c	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_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..df9dc77c7002
--- /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.python.org/pypi/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	372bbe39047c0a2550319a3a82f3e063	multibuild	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	xdg-utils	f2c8335407f0b935b0a96d4adf23ef25
+_md5_=1322b37268b445a85ac3c6de2d87c1f1
diff --git a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r2 b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r2
new file mode 100644
index 000000000000..862ae6198b6a
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r2
@@ -0,0 +1,12 @@
+DEFINED_PHASES=compile install prepare
+DEPEND=dev-lang/perl sci-biology/hmmer
+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
+SLOT=0
+SRC_URI=mirror://gentoo/qrna-2.0.3c.tar.bz2
+_eclasses_=multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=35f5a46d4490059eb478c8a8c7998ac5
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..7e699f90d35c
--- /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_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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/recon-1.08 b/metadata/md5-cache/sci-biology/recon-1.08
new file mode 100644
index 000000000000..015510313e30
--- /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	185a06792159ca143528e7010368e8af
+_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..e23146dd18d5
--- /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
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	flag-o-matic	2274fcc1e7ef6affaff5bcd636275417	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=7aa6de8741afab9d848f4cbada44c7ad
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..157c940fd745
--- /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	185a06792159ca143528e7010368e8af
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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..ebd5a2645185
--- /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_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_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	317a2557b4d7319a7418225f65accf77	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af
+_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..b8a41213725f
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/samtools-1.5
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+DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats
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+HOMEPAGE=http://www.htslib.org/
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+LICENSE=MIT
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+SRC_URI=mirror://sourceforge/samtools/samtools-1.5.tar.bz2
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diff --git a/metadata/md5-cache/sci-biology/seaview-4.3.5 b/metadata/md5-cache/sci-biology/seaview-4.3.5
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index 000000000000..2cfdef66e81e
--- /dev/null
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+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
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+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
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new file mode 100644
index 000000000000..e8bdbb226211
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+++ b/metadata/md5-cache/sci-biology/seaview-4.6
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+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
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diff --git a/metadata/md5-cache/sci-biology/seqan-1.4.2-r1 b/metadata/md5-cache/sci-biology/seqan-1.4.2-r1
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index 000000000000..95f3916eadab
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+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-3.7.2
+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
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index 000000000000..edbb182cef4b
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+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
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new file mode 100644
index 000000000000..531710373349
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+++ b/metadata/md5-cache/sci-biology/shrimp-2.0.1
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+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
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index 000000000000..493770a58d7f
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+DEPEND=!sci-mathematics/cado-nfs
+DESCRIPTION=SHort Read Mapping Package
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+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_python2_7(+)]
+REQUIRED_USE=python_targets_python2_7
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new file mode 100644
index 000000000000..be1a3c034497
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+++ b/metadata/md5-cache/sci-biology/sibsim4-0.20
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+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	185a06792159ca143528e7010368e8af
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diff --git a/metadata/md5-cache/sci-biology/sim4-20030921-r2 b/metadata/md5-cache/sci-biology/sim4-20030921-r2
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index 000000000000..eba274b723fc
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+++ b/metadata/md5-cache/sci-biology/sim4-20030921-r2
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+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
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index 000000000000..2f11c85ad00b
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/snpfile-2.0.1-r2
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+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-1.15:1.15 ) >=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:=
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+SRC_URI=http://www.birc.au.dk/~mailund/SNPFile/download/snpfile-2.0.1.tar.gz
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index 000000000000..42ed5e1dff06
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+++ b/metadata/md5-cache/sci-biology/stride-20011129-r1
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+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
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+HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+IUSE=examples
+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/Stable/Version_11.00.8cbe486/T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz
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+DEPEND=virtual/fortran
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+LICENSE=GPL-2
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@@ -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_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_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_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-1.15:1.15 ) >=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_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_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_python2_7(+)] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2
+REQUIRED_USE=python_targets_python2_7
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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
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+DEFINED_PHASES=compile install
+DEPEND=emboss? ( sci-biology/emboss )
+DESCRIPTION=A database of eucaryotic transcription factors
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+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
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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..aa6b4a768139
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/tree-puzzle-5.2
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+DEFINED_PHASES=configure install prepare setup
+DEPEND=mpi? ( virtual/mpi )
+DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data
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+HOMEPAGE=http://www.tree-puzzle.de
+IUSE=mpi
+KEYWORDS=~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos
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index 000000000000..cdeb58434903
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+DESCRIPTION=A phylogenetic tree viewer
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+HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/
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+RDEPEND=x11-libs/wxGTK:3.0[X]
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+SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz
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--- /dev/null
+++ b/metadata/md5-cache/sci-biology/trf-4.04-r1
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+++ b/metadata/md5-cache/sci-biology/trnascan-se-1.31
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+HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/
+KEYWORDS=amd64 x86
+LICENSE=GPL-2
+SLOT=0
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new file mode 100644
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+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
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+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 )
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+SRC_URI=http://hgdownload.cse.ucsc.edu/admin/jksrc.v260.zip
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+HOMEPAGE=http://mfold.rna.albany.edu/
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+KEYWORDS=~amd64 ~x86
+LICENSE=unafold
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+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
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index 000000000000..cc22d030d2c1
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+++ b/metadata/md5-cache/sci-biology/vaal-46233-r2
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+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-1.15:1.15 ) >=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
+_eclasses_=autotools	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
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index 000000000000..0546c57465ad
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+DESCRIPTION=Tools for working with VCF (Variant Call Format) files
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+HOMEPAGE=http://vcftools.sourceforge.net/
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+KEYWORDS=~x86 ~amd64
+LICENSE=LGPL-3
+RDEPEND=sys-libs/zlib dev-lang/perl:= lapack? ( virtual/lapack )
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+DEPEND=sys-libs/zlib doc? ( virtual/latex-base )
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+HOMEPAGE=http://www.ebi.ac.uk/~zerbino/velvet/
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+DESCRIPTION=RNA secondary structure prediction and comparison
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+HOMEPAGE=http://www.tbi.univie.ac.at/~ivo/RNA/
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+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? ( || ( python_targets_python2_7 ) )
+SLOT=0
+SRC_URI=http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-2.1.1.tar.gz
+_eclasses_=autotools	dc412f38566b91012efd58b9c203e6c3	autotools-utils	5a4611dfba155b1659528663fad4cd5e	distutils-r1	372bbe39047c0a2550319a3a82f3e063	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multibuild	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70	xdg-utils	f2c8335407f0b935b0a96d4adf23ef25
+_md5_=1e58c830b49ced05ae9960fcc2dead13
diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.8 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.8
new file mode 100644
index 000000000000..e2774ee89910
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/vienna-rna-2.1.8
@@ -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-1.15:1.15 ) >=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? ( || ( python_targets_python2_7 ) )
+SLOT=0
+SRC_URI=http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz
+_eclasses_=autotools	dc412f38566b91012efd58b9c203e6c3	autotools-utils	5a4611dfba155b1659528663fad4cd5e	distutils-r1	372bbe39047c0a2550319a3a82f3e063	epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	libtool	0081a71a261724730ec4c248494f044d	ltprune	2770eed66a9b8ef944714cd0e968182e	multibuild	72647e255187a1fadc81097b3657e5c3	multilib	97f470f374f2e94ccab04a2fb21d811e	multiprocessing	6f5991c7101863d0b29df63990ad852e	perl-functions	01e8c68d5a528bbcda4d3c60205983df	perl-module	863b35d127db98823d439f8d73c2d011	python-r1	e9350ec46bb5c9f3504b4fbe8b8d8987	python-utils-r1	c9de01becf9df3f8c10aeec3dc693f5d	toolchain-funcs	185a06792159ca143528e7010368e8af	unpacker	f40f7b4bd5aa88c2a4ba7b0d1e0ded70	xdg-utils	f2c8335407f0b935b0a96d4adf23ef25
+_md5_=b2a6486af275e75c6365ab7eeba1e0bd
diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1 b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1
new file mode 100644
index 000000000000..092ab79ca038
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r1
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile configure install prepare
+DEPEND=x11-libs/libXt !x11-terms/terminator
+DESCRIPTION=The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG
+EAPI=4
+HOMEPAGE=https://sourceforge.net/projects/wgs-assembler/
+IUSE=static-libs
+KEYWORDS=amd64 x86
+LICENSE=GPL-2
+RDEPEND=x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl
+SLOT=0
+SRC_URI=mirror://sourceforge/wgs-assembler/wgs-7.0.tar.bz2
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=6ebc94c9eb0083edd0308af8a336afe0
diff --git a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha
new file mode 100644
index 000000000000..af74e8caa815
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha
@@ -0,0 +1,13 @@
+DEFINED_PHASES=compile install prepare test
+DEPEND=~sci-biology/hmmer-2.3.2 app-shells/tcsh dev-lang/perl virtual/latex-base
+DESCRIPTION=Intelligent algorithms for DNA searches
+EAPI=5
+HOMEPAGE=http://www.ebi.ac.uk/Wise2/
+IUSE=doc static-libs
+KEYWORDS=~amd64 ~x86
+LICENSE=BSD
+RDEPEND=~sci-biology/hmmer-2.3.2
+SLOT=0
+SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/wise2/wise2.4.0alpha.tar.gz
+_eclasses_=epatch	8233751dc5105a6ae8fcd86ce2bb0247	estack	43ddf5aaffa7a8d0482df54d25a66a1f	eutils	227b041a120d309fdefbebb3b8c1dfa9	ltprune	2770eed66a9b8ef944714cd0e968182e	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af	versionator	c80ccf29e90adea7c5cae94b42eb76d0
+_md5_=3fc50009d15dddcf126bbf0735404920
diff --git a/metadata/md5-cache/sci-biology/yass-1.14-r2 b/metadata/md5-cache/sci-biology/yass-1.14-r2
new file mode 100644
index 000000000000..a363d14571c6
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/yass-1.14-r2
@@ -0,0 +1,13 @@
+DEFINED_PHASES=configure prepare
+DEPEND=dmalloc? ( dev-libs/dmalloc ) >=app-portage/elt-patches-20170422 !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4
+DESCRIPTION=Genomic similarity search with multiple transition constrained spaced seeds
+EAPI=6
+HOMEPAGE=http://bioinfo.lifl.fr/yass/
+IUSE=dmalloc lowmem threads
+KEYWORDS=~amd64 ~x86
+LICENSE=GPL-2
+RDEPEND=dmalloc? ( dev-libs/dmalloc )
+SLOT=0
+SRC_URI=http://bioinfo.lifl.fr/yass/files/yass-1.14.tar.gz
+_eclasses_=autotools	dc412f38566b91012efd58b9c203e6c3	libtool	0081a71a261724730ec4c248494f044d	multilib	97f470f374f2e94ccab04a2fb21d811e	toolchain-funcs	185a06792159ca143528e7010368e8af
+_md5_=3a4ba9b4e7b8efec51cfc79d261fefd3
author	V3n3RiX <venerix@redcorelinux.org>	2017-10-09 18:53:29 +0100
committer	V3n3RiX <venerix@redcorelinux.org>	2017-10-09 18:53:29 +0100
commit	4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch)
tree	ba5f07bf3f9d22d82e54a462313f5d244036c768 /metadata/md5-cache/sci-biology