From f8999218b5a6eafa151e7367030cbfdb69e045ed Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 25 May 2024 00:07:14 +0100 Subject: gentoo auto-resync : 25:05:2024 - 00:07:14 --- metadata/md5-cache/sci-biology/Manifest.gz | Bin 22343 -> 22341 bytes metadata/md5-cache/sci-biology/bcftools-1.17 | 16 ---------------- metadata/md5-cache/sci-biology/bcftools-1.20 | 16 ++++++++++++++++ metadata/md5-cache/sci-biology/pysam-0.21.0 | 17 ----------------- metadata/md5-cache/sci-biology/pysam-0.22.1 | 17 +++++++++++++++++ metadata/md5-cache/sci-biology/raxml-7.2.6 | 13 ------------- metadata/md5-cache/sci-biology/raxml-8.2.13 | 12 ++++++++++++ metadata/md5-cache/sci-biology/samtools-1.17 | 14 -------------- metadata/md5-cache/sci-biology/samtools-1.20 | 14 ++++++++++++++ 9 files changed, 59 insertions(+), 60 deletions(-) delete mode 100644 metadata/md5-cache/sci-biology/bcftools-1.17 create mode 100644 metadata/md5-cache/sci-biology/bcftools-1.20 delete mode 100644 metadata/md5-cache/sci-biology/pysam-0.21.0 create mode 100644 metadata/md5-cache/sci-biology/pysam-0.22.1 delete mode 100644 metadata/md5-cache/sci-biology/raxml-7.2.6 create mode 100644 metadata/md5-cache/sci-biology/raxml-8.2.13 delete mode 100644 metadata/md5-cache/sci-biology/samtools-1.17 create mode 100644 metadata/md5-cache/sci-biology/samtools-1.20 (limited to 'metadata/md5-cache/sci-biology') diff --git a/metadata/md5-cache/sci-biology/Manifest.gz b/metadata/md5-cache/sci-biology/Manifest.gz index 4c65c258b812..016461d56d5c 100644 Binary files a/metadata/md5-cache/sci-biology/Manifest.gz and b/metadata/md5-cache/sci-biology/Manifest.gz differ diff --git a/metadata/md5-cache/sci-biology/bcftools-1.17 b/metadata/md5-cache/sci-biology/bcftools-1.17 deleted file mode 100644 index 97bb25ddd980..000000000000 --- a/metadata/md5-cache/sci-biology/bcftools-1.17 +++ /dev/null @@ -1,16 +0,0 @@ -BDEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) -DEFINED_PHASES=configure prepare setup -DEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) =sci-libs/htslib-1.17*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) -DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files -EAPI=8 -HOMEPAGE=http://www.htslib.org -INHERIT=python-single-r1 -IUSE=python_single_target_python3_10 python_single_target_python3_11 -KEYWORDS=~amd64 ~x86 -LICENSE=MIT -RDEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) =sci-libs/htslib-1.17*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) -REQUIRED_USE=^^ ( python_single_target_python3_10 python_single_target_python3_11 ) -SLOT=0 -SRC_URI=https://github.com/samtools/bcftools/releases/download/1.17/bcftools-1.17.tar.bz2 -_eclasses_=multilib c19072c3cd7ac5cb21de013f7e9832e0 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe python-single-r1 75118e916668a74c660a13b0ecb22562 python-utils-r1 8b220bbce5c119fb1d4d5c2f5588f3ea toolchain-funcs e56c7649b804f051623c8bc1a1c44084 -_md5_=5271780ace94107aae357a985f191e14 diff --git a/metadata/md5-cache/sci-biology/bcftools-1.20 b/metadata/md5-cache/sci-biology/bcftools-1.20 new file mode 100644 index 000000000000..dc122534cec9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bcftools-1.20 @@ -0,0 +1,16 @@ +BDEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 ) +DEFINED_PHASES=configure prepare setup +DEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) python_single_target_python3_12? ( dev-python/matplotlib[python_targets_python3_12(-)] ) =sci-libs/htslib-1.20*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 ) +DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files +EAPI=8 +HOMEPAGE=http://www.htslib.org +INHERIT=python-single-r1 +IUSE=python_single_target_python3_10 python_single_target_python3_11 python_single_target_python3_12 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) python_single_target_python3_12? ( dev-python/matplotlib[python_targets_python3_12(-)] ) =sci-libs/htslib-1.20*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 ) +REQUIRED_USE=^^ ( python_single_target_python3_10 python_single_target_python3_11 python_single_target_python3_12 ) +SLOT=0 +SRC_URI=https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2 +_eclasses_=multilib c19072c3cd7ac5cb21de013f7e9832e0 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe python-single-r1 75118e916668a74c660a13b0ecb22562 python-utils-r1 8b220bbce5c119fb1d4d5c2f5588f3ea toolchain-funcs e56c7649b804f051623c8bc1a1c44084 +_md5_=88036066dfeb432f0a530195f08f59f7 diff --git a/metadata/md5-cache/sci-biology/pysam-0.21.0 b/metadata/md5-cache/sci-biology/pysam-0.21.0 deleted file mode 100644 index 9c15d61f31a6..000000000000 --- a/metadata/md5-cache/sci-biology/pysam-0.21.0 +++ /dev/null @@ -1,17 +0,0 @@ -BDEPEND=test? ( =sci-biology/bcftools-1.17* =sci-biology/samtools-1.17* ) test? ( =sci-libs/htslib-1.17*:= >=dev-python/pytest-7.4.4[python_targets_python3_10(-)?,python_targets_python3_11(-)?] ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?] -DEFINED_PHASES=compile configure install prepare test -DEPEND==sci-libs/htslib-1.17*:= dev-python/cython[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/setuptools[python_targets_python3_10(-)?,python_targets_python3_11(-)?] -DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format -EAPI=8 -HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/ -INHERIT=distutils-r1 -IUSE=test python_targets_python3_10 python_targets_python3_11 -KEYWORDS=~amd64 ~x86 -LICENSE=MIT -RDEPEND==sci-libs/htslib-1.17*:= python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) -REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 ) -RESTRICT=!test? ( test ) -SLOT=0 -SRC_URI=https://github.com/pysam-developers/pysam/archive/v0.21.0.tar.gz -> pysam-0.21.0.gh.tar.gz -_eclasses_=distutils-r1 5400d21736d8621562bf93be4fa98eec flag-o-matic d309b9713dfc18e754cba88d3ba69653 multibuild d67e78a235f541871c7dfe4cf7931489 multilib c19072c3cd7ac5cb21de013f7e9832e0 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 2df4e452cea39a9ec8fb543ce059f8d6 out-of-source-utils 1a9007554652a6e627edbccb3c25a439 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f python-utils-r1 8b220bbce5c119fb1d4d5c2f5588f3ea toolchain-funcs e56c7649b804f051623c8bc1a1c44084 -_md5_=d2f337ee806641d85739cd55c8698806 diff --git a/metadata/md5-cache/sci-biology/pysam-0.22.1 b/metadata/md5-cache/sci-biology/pysam-0.22.1 new file mode 100644 index 000000000000..1e11f68d7d5b --- /dev/null +++ b/metadata/md5-cache/sci-biology/pysam-0.22.1 @@ -0,0 +1,17 @@ +BDEPEND=dev-python/cython[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] test? ( =sci-biology/bcftools-1.20* =sci-biology/samtools-1.20* ) test? ( =sci-libs/htslib-1.20*:= >=dev-python/pytest-7.4.4[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 ) >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] +DEFINED_PHASES=compile configure install prepare test +DEPEND==sci-libs/htslib-1.20*:= dev-python/setuptools[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] +DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format +EAPI=8 +HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/ +INHERIT=distutils-r1 +IUSE=test python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND==sci-libs/htslib-1.20*:= python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 ) +REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/pysam-developers/pysam/archive/v0.22.1.tar.gz -> pysam-0.22.1.gh.tar.gz +_eclasses_=distutils-r1 5400d21736d8621562bf93be4fa98eec flag-o-matic d309b9713dfc18e754cba88d3ba69653 multibuild d67e78a235f541871c7dfe4cf7931489 multilib c19072c3cd7ac5cb21de013f7e9832e0 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 2df4e452cea39a9ec8fb543ce059f8d6 out-of-source-utils 1a9007554652a6e627edbccb3c25a439 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f python-utils-r1 8b220bbce5c119fb1d4d5c2f5588f3ea toolchain-funcs e56c7649b804f051623c8bc1a1c44084 +_md5_=a742eeecf26e6de57df273759b8491aa diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-7.2.6 deleted file mode 100644 index 3439f6b6df23..000000000000 --- a/metadata/md5-cache/sci-biology/raxml-7.2.6 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile configure install -DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees -EAPI=7 -HOMEPAGE=http://wwwkramer.in.tum.de/exelixis/software.html -INHERIT=flag-o-matic toolchain-funcs -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_=flag-o-matic d309b9713dfc18e754cba88d3ba69653 multilib c19072c3cd7ac5cb21de013f7e9832e0 toolchain-funcs e56c7649b804f051623c8bc1a1c44084 -_md5_=14b77d8b019468c10a65f1358be0d8ae diff --git a/metadata/md5-cache/sci-biology/raxml-8.2.13 b/metadata/md5-cache/sci-biology/raxml-8.2.13 new file mode 100644 index 000000000000..560edd6c6a8a --- /dev/null +++ b/metadata/md5-cache/sci-biology/raxml-8.2.13 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees +EAPI=8 +HOMEPAGE=https://github.com/stamatak/standard-RAxML +INHERIT=flag-o-matic toolchain-funcs +IUSE=cpu_flags_x86_sse3 +threads +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://github.com/stamatak/standard-RAxML/archive/refs/tags/v8.2.13.tar.gz -> raxml-8.2.13.tar.gz +_eclasses_=flag-o-matic d309b9713dfc18e754cba88d3ba69653 multilib c19072c3cd7ac5cb21de013f7e9832e0 toolchain-funcs e56c7649b804f051623c8bc1a1c44084 +_md5_=b1b4de0bedc435411038a43f078ba175 diff --git a/metadata/md5-cache/sci-biology/samtools-1.17 b/metadata/md5-cache/sci-biology/samtools-1.17 deleted file mode 100644 index bcb720f8e8e9..000000000000 --- a/metadata/md5-cache/sci-biology/samtools-1.17 +++ /dev/null @@ -1,14 +0,0 @@ -BDEPEND=virtual/pkgconfig -DEFINED_PHASES=compile configure install prepare -DEPEND=dev-lang/perl =sci-libs/htslib-1.17*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib -DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats -EAPI=8 -HOMEPAGE=http://www.htslib.org/ -INHERIT=toolchain-funcs -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos -LICENSE=MIT -RDEPEND=dev-lang/perl =sci-libs/htslib-1.17*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib -SLOT=0 -SRC_URI=https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 -_eclasses_=multilib c19072c3cd7ac5cb21de013f7e9832e0 toolchain-funcs e56c7649b804f051623c8bc1a1c44084 -_md5_=d899fa7ac2ab4404dcca131cb83b93ab diff --git a/metadata/md5-cache/sci-biology/samtools-1.20 b/metadata/md5-cache/sci-biology/samtools-1.20 new file mode 100644 index 000000000000..7938609b9903 --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.20 @@ -0,0 +1,14 @@ +BDEPEND=virtual/pkgconfig +DEFINED_PHASES=compile configure install prepare +DEPEND=dev-lang/perl =sci-libs/htslib-1.20*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib +DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats +EAPI=8 +HOMEPAGE=http://www.htslib.org/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=MIT +RDEPEND=dev-lang/perl =sci-libs/htslib-1.20*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib +SLOT=0 +SRC_URI=https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2 +_eclasses_=multilib c19072c3cd7ac5cb21de013f7e9832e0 toolchain-funcs e56c7649b804f051623c8bc1a1c44084 +_md5_=582b7ec64e75c223a70f748cfa2d9bca -- cgit v1.2.3