diff options
Diffstat (limited to 'metadata/md5-cache/sci-biology')
126 files changed, 1696 insertions, 0 deletions
diff --git a/metadata/md5-cache/sci-biology/HTSeq-2.0.2 b/metadata/md5-cache/sci-biology/HTSeq-2.0.2 new file mode 100644 index 000000000000..b141e1e9f019 --- /dev/null +++ b/metadata/md5-cache/sci-biology/HTSeq-2.0.2 @@ -0,0 +1,17 @@ +BDEPEND=>=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python3_10(-)?,python_targets_python3_11(-)?] test? ( dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] sci-biology/pysam[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/pytest-7.3.1[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-67.8.0-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] +DEFINED_PHASES=compile configure install prepare test +DEPEND=dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] sci-biology/pysam[python_targets_python3_10(-)?,python_targets_python3_11(-)?] test? ( dev-python/matplotlib[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pandas[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/scipy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] ) +DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files +EAPI=8 +HOMEPAGE=https://htseq.readthedocs.io/ +INHERIT=distutils-r1 flag-o-matic +IUSE=test python_targets_python3_10 python_targets_python3_11 +KEYWORDS=~amd64 +LICENSE=GPL-3+ +RDEPEND=dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] sci-biology/pysam[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 ) +REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/htseq/htseq/archive/release_2.0.2.tar.gz -> HTSeq-2.0.2.gh.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc out-of-source-utils 1a9007554652a6e627edbccb3c25a439 multibuild 30dbf3c5a31db09a19f31ad0a68f2405 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f distutils-r1 d05609532b134be7c4ae2514f4c7d06e +_md5_=29d76005d4f5d0a05fc0182fba12f7f5 diff --git a/metadata/md5-cache/sci-biology/HTSeq-9999 b/metadata/md5-cache/sci-biology/HTSeq-9999 new file mode 100644 index 000000000000..07ba565f4da6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/HTSeq-9999 @@ -0,0 +1,16 @@ +BDEPEND=>=dev-lang/swig-3.0.8 dev-python/cython[python_targets_python3_10(-)?,python_targets_python3_11(-)?] test? ( dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] sci-biology/pysam[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/pytest-7.3.1[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-67.8.0-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-vcs/git-1.8.2.1[curl] +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] sci-biology/pysam[python_targets_python3_10(-)?,python_targets_python3_11(-)?] test? ( dev-python/matplotlib[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pandas[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/scipy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] ) +DESCRIPTION=Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files +EAPI=8 +HOMEPAGE=https://htseq.readthedocs.io/ +INHERIT=distutils-r1 flag-o-matic git-r3 +IUSE=test python_targets_python3_10 python_targets_python3_11 +LICENSE=GPL-3+ +PROPERTIES=live +RDEPEND=dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] sci-biology/pysam[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 ) +REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 ) +RESTRICT=!test? ( test ) +SLOT=0 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc out-of-source-utils 1a9007554652a6e627edbccb3c25a439 multibuild 30dbf3c5a31db09a19f31ad0a68f2405 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f distutils-r1 d05609532b134be7c4ae2514f4c7d06e git-r3 2358a7b20091609e24bd3a83b3ac5991 +_md5_=29d76005d4f5d0a05fc0182fba12f7f5 diff --git a/metadata/md5-cache/sci-biology/STAR-2.7.10a b/metadata/md5-cache/sci-biology/STAR-2.7.10a new file mode 100644 index 000000000000..1d645f05ee44 --- /dev/null +++ b/metadata/md5-cache/sci-biology/STAR-2.7.10a @@ -0,0 +1,14 @@ +BDEPEND=virtual/pkgconfig +DEFINED_PHASES=compile configure install prepare pretend setup +DEPEND=sci-libs/htslib:= +DESCRIPTION=STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays +EAPI=8 +HOMEPAGE=https://github.com/alexdobin/STAR +INHERIT=toolchain-funcs +KEYWORDS=~amd64 +LICENSE=GPL-3 +RDEPEND=sci-libs/htslib:= +SLOT=0 +SRC_URI=https://github.com/alexdobin/STAR/archive/2.7.10a.tar.gz -> STAR-2.7.10a.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=521aed057c81cfa841ab4b2dcf63e65b diff --git a/metadata/md5-cache/sci-biology/aaindex-9.1-r2 b/metadata/md5-cache/sci-biology/aaindex-9.1-r2 new file mode 100644 index 000000000000..6ba6ecc0082a --- /dev/null +++ b/metadata/md5-cache/sci-biology/aaindex-9.1-r2 @@ -0,0 +1,12 @@ +BDEPEND=emboss? ( sci-biology/emboss ) +DEFINED_PHASES=compile install +DESCRIPTION=Amino acid indices and similarity matrices +EAPI=8 +HOMEPAGE=https://www.genome.jp/aaindex/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=mirror://gentoo/aaindex-9.1.tar.bz2 +_md5_=881d3a5590b0d557e474f7686f0ab42c diff --git a/metadata/md5-cache/sci-biology/abyss-2.3.4 b/metadata/md5-cache/sci-biology/abyss-2.3.4 new file mode 100644 index 000000000000..aafe62b1316b --- /dev/null +++ b/metadata/md5-cache/sci-biology/abyss-2.3.4 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure prepare pretend setup +DEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= dev-libs/libffi:0= ) sys-cluster/openmpi dev-db/sqlite:3 misc-haskell? ( dev-lang/ghc ) +DESCRIPTION=Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +EAPI=8 +HOMEPAGE=https://www.bcgsc.ca/resources/software/abyss/ +INHERIT=autotools toolchain-funcs +IUSE=openmp misc-haskell +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=dev-cpp/sparsehash dev-libs/boost:= misc-haskell? ( dev-libs/gmp:0= dev-libs/libffi:0= ) sys-cluster/openmpi dev-db/sqlite:3 +SLOT=0 +SRC_URI=https://github.com/bcgsc/abyss/archive/2.3.4.tar.gz -> abyss-2.3.4.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=9a708eff89b221551fbb0bcc299ccfa3 diff --git a/metadata/md5-cache/sci-biology/amap-2.2-r5 b/metadata/md5-cache/sci-biology/amap-2.2-r5 new file mode 100644 index 000000000000..3ab2568482f6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/amap-2.2-r5 @@ -0,0 +1,15 @@ +BDEPEND=java? ( >=virtual/jre-1.8:* ) +DEFINED_PHASES=compile configure install preinst prepare setup +DEPEND=java? ( >=dev-java/java-config-2.2.0-r3 ) java? ( >=dev-java/ant-core-1.8.2:0 dev-java/javatoolkit ) +DESCRIPTION=Protein multiple-alignment-based sequence annealing +EAPI=8 +HOMEPAGE=https://wiki.gentoo.org/wiki/No_homepage +INHERIT=java-pkg-opt-2 java-ant-2 toolchain-funcs +IUSE=java java +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=java? ( >=virtual/jre-1.8:* ) 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_=java-utils-2 30b5d143e64d691346fcdd85eef1c614 java-pkg-opt-2 3816f3fc28ed2b067845e2802eb954b2 multilib c19072c3cd7ac5cb21de013f7e9832e0 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc java-ant-2 19239227fab7816f57abbc0c7d819396 +_md5_=b4e132581d5e91612a875f7f94387a1b 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..07a79bb6d279 --- /dev/null +++ b/metadata/md5-cache/sci-biology/augustus-2.5.5 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Eukaryotic gene predictor +EAPI=7 +HOMEPAGE=http://augustus.gobics.de/ +INHERIT=toolchain-funcs +IUSE=examples +KEYWORDS=amd64 ~x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=4c500e601e76f119e63d2dc13321648c diff --git a/metadata/md5-cache/sci-biology/augustus-3.4.0-r3 b/metadata/md5-cache/sci-biology/augustus-3.4.0-r3 new file mode 100644 index 000000000000..b6d7ebbde37c --- /dev/null +++ b/metadata/md5-cache/sci-biology/augustus-3.4.0-r3 @@ -0,0 +1,15 @@ +BDEPEND=doc? ( app-doc/doxygen ) +DEFINED_PHASES=compile install +DEPEND=dev-db/sqlite:3 dev-db/mysql++:= dev-db/mysql-connector-c:= dev-libs/boost:=[zlib] sci-biology/bamtools:= sci-biology/samtools:0 sci-libs/gsl:= sci-libs/htslib:= sci-libs/suitesparse sci-mathematics/lpsolve:= sys-libs/zlib +DESCRIPTION=Eukaryotic gene predictor +EAPI=8 +HOMEPAGE=https://bioinf.uni-greifswald.de/augustus/ +INHERIT=docs toolchain-funcs +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=dev-db/sqlite:3 dev-db/mysql++:= dev-db/mysql-connector-c:= dev-libs/boost:=[zlib] sci-biology/bamtools:= sci-biology/samtools:0 sci-libs/gsl:= sci-libs/htslib:= sci-libs/suitesparse sci-mathematics/lpsolve:= sys-libs/zlib +SLOT=0 +SRC_URI=https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v3.4.0.tar.gz -> augustus-3.4.0.tar.gz +_eclasses_=docs 74475974eae5130ba3e19b31b8ae46b8 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=5af682d1467b7eddf54bfe603492b4fa diff --git a/metadata/md5-cache/sci-biology/bamtools-2.5.2 b/metadata/md5-cache/sci-biology/bamtools-2.5.2 new file mode 100644 index 000000000000..ae11dcf38c13 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-2.5.2 @@ -0,0 +1,14 @@ +BDEPEND=virtual/pkgconfig >=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=7 +HOMEPAGE=https://github.com/pezmaster31/bamtools +INHERIT=cmake +KEYWORDS=~amd64 ~x86 +LICENSE=MIT +RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +SLOT=0/2.5.2 +SRC_URI=https://github.com/pezmaster31/bamtools/archive/v2.5.2.tar.gz -> bamtools-2.5.2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 xdg-utils baea6080dd821f5562d715887954c9d3 cmake fc2f89084f590ac95c004ea95b0d2f80 +_md5_=efdfbdbf4181a018ee9965d5c16be71f diff --git a/metadata/md5-cache/sci-biology/bamtools-9999 b/metadata/md5-cache/sci-biology/bamtools-9999 new file mode 100644 index 000000000000..829ba8832dff --- /dev/null +++ b/metadata/md5-cache/sci-biology/bamtools-9999 @@ -0,0 +1,13 @@ +BDEPEND=virtual/pkgconfig >=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 >=dev-vcs/git-1.8.2.1[curl] +DEFINED_PHASES=compile configure install prepare test unpack +DEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +DESCRIPTION=A programmer's API and an end-user's toolkit for handling BAM files +EAPI=7 +HOMEPAGE=https://github.com/pezmaster31/bamtools +INHERIT=cmake git-r3 +LICENSE=MIT +PROPERTIES=live +RDEPEND=>=dev-libs/jsoncpp-1.8.0:= sys-libs/zlib:= +SLOT=0/9999 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 xdg-utils baea6080dd821f5562d715887954c9d3 cmake fc2f89084f590ac95c004ea95b0d2f80 git-r3 2358a7b20091609e24bd3a83b3ac5991 +_md5_=a2299dc6ca850c1c25582656d7586681 diff --git a/metadata/md5-cache/sci-biology/bcftools-1.17 b/metadata/md5-cache/sci-biology/bcftools-1.17 new file mode 100644 index 000000000000..e45d1dce14bb --- /dev/null +++ b/metadata/md5-cache/sci-biology/bcftools-1.17 @@ -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 ) +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_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-single-r1 75118e916668a74c660a13b0ecb22562 +_md5_=5271780ace94107aae357a985f191e14 diff --git a/metadata/md5-cache/sci-biology/bedtools-2.30.0 b/metadata/md5-cache/sci-biology/bedtools-2.30.0 new file mode 100644 index 000000000000..43f740d27789 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bedtools-2.30.0 @@ -0,0 +1,16 @@ +BDEPEND=|| ( dev-lang/python:3.11 dev-lang/python:3.10 ) test? ( >=sci-biology/samtools-1.10:0 ) +DEFINED_PHASES=configure install setup +DEPEND=app-arch/bzip2 app-arch/xz-utils sys-libs/zlib +DESCRIPTION=Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats +EAPI=8 +HOMEPAGE=https://bedtools.readthedocs.io/ +INHERIT=python-any-r1 toolchain-funcs +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=app-arch/bzip2 app-arch/xz-utils sys-libs/zlib +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools-2.30.0.tar.gz +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-any-r1 f5169813d1619761b459800587005fd2 +_md5_=6362b2cc40163766b0448cea57894c3a 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..07a3a8ee20aa --- /dev/null +++ b/metadata/md5-cache/sci-biology/bfast-0.7.0a @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=prepare +DESCRIPTION=Blat-like Fast Accurate Search Tool +EAPI=7 +HOMEPAGE=https://sourceforge.net/projects/bfast/ +INHERIT=autotools +IUSE=test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-perl/XML-Simple +RESTRICT=test +SLOT=0 +SRC_URI=mirror://sourceforge/bfast/bfast-0.7.0a.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=e64abecddb86e9860edc80410f299d83 diff --git a/metadata/md5-cache/sci-biology/biogrep-1.0-r3 b/metadata/md5-cache/sci-biology/biogrep-1.0-r3 new file mode 100644 index 000000000000..a3a1bfc5feb3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biogrep-1.0-r3 @@ -0,0 +1,13 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=install prepare +DESCRIPTION=Multithreaded tool for matching large sets of patterns against biosequence DBs +EAPI=8 +HOMEPAGE=http://stephanopoulos.openwetware.org/BIOGREP.html +INHERIT=autotools +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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=18fc653ace8feaf53e4d1c1818b7b00c diff --git a/metadata/md5-cache/sci-biology/biopandas-0.4.1 b/metadata/md5-cache/sci-biology/biopandas-0.4.1 new file mode 100644 index 000000000000..8cc85acdb5c2 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopandas-0.4.1 @@ -0,0 +1,16 @@ +BDEPEND=test? ( dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pandas[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/nose-1.3.7_p20221026[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/gpep517-15[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/setuptools-67.8.0-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] +DEFINED_PHASES=compile configure install prepare test +DESCRIPTION=Molecular Structures in Pandas DataFrames +EAPI=8 +HOMEPAGE=https://rasbt.github.io/biopandas/ https://github.com/BioPandas/biopandas https://pypi.org/project/biopandas/ +INHERIT=distutils-r1 +IUSE=test python_targets_python3_10 python_targets_python3_11 +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pandas[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 ) +REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/BioPandas/biopandas/archive/refs/tags/v0.4.1.tar.gz -> biopandas-0.4.1.gh.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc out-of-source-utils 1a9007554652a6e627edbccb3c25a439 multibuild 30dbf3c5a31db09a19f31ad0a68f2405 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f distutils-r1 d05609532b134be7c4ae2514f4c7d06e +_md5_=3b87692064234ef962aa52c8f93f9e17 diff --git a/metadata/md5-cache/sci-biology/bioperl-1.6.9-r1 b/metadata/md5-cache/sci-biology/bioperl-1.6.9-r1 new file mode 100644 index 000000000000..0d662ae7c43d --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-1.6.9-r1 @@ -0,0 +1,18 @@ +BDEPEND=dev-perl/Module-Build dev-lang/perl test? ( >=virtual/perl-Test-Simple-1 ) +DEFINED_PHASES=compile configure install prepare test +DEPEND=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 +DESCRIPTION=Perl tools for bioinformatics - Core modules +EAPI=8 +HOMEPAGE=http://www.bioperl.org/ +INHERIT=perl-module +IUSE=minimal graphviz sqlite +db +network +run test +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:= +REQUIRED_USE=minimal? ( !graphviz ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe perl-functions c3fca037246e877693badea0df3b0ef8 readme.gentoo-r1 204091a2cde6179cd9d3db26d09412d3 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 perl-module 4e37e1004a0a27e41bb7025c0b974676 +_md5_=275c67756e8440c392c02c29c75e1388 diff --git a/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r2 b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r2 new file mode 100644 index 000000000000..b0965f849955 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-db-1.6.9-r2 @@ -0,0 +1,16 @@ +BDEPEND=dev-perl/Module-Build dev-lang/perl test? ( >=virtual/perl-Test-Simple-1 ) +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=sci-biology/bioperl-1.6.9 dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql 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=8 +HOMEPAGE=http://www.bioperl.org/ +INHERIT=perl-module +IUSE=test 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 !test? ( test ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe perl-functions c3fca037246e877693badea0df3b0ef8 readme.gentoo-r1 204091a2cde6179cd9d3db26d09412d3 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 perl-module 4e37e1004a0a27e41bb7025c0b974676 +_md5_=56259564f94ae015e0cdd27bc2db8b21 diff --git a/metadata/md5-cache/sci-biology/bioperl-network-1.6.9-r1 b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9-r1 new file mode 100644 index 000000000000..e6315bb51d36 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-network-1.6.9-r1 @@ -0,0 +1,16 @@ +BDEPEND=dev-perl/Module-Build dev-lang/perl test? ( >=virtual/perl-Test-Simple-1 ) +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl +DESCRIPTION=Perl tools for bioinformatics - Analysis of protein-protein interaction networks +EAPI=8 +HOMEPAGE=http://www.bioperl.org/ +INHERIT=perl-module +IUSE=test +KEYWORDS=amd64 ~x86 +LICENSE=|| ( Artistic GPL-1+ ) +RDEPEND=>=sci-biology/bioperl-1.6.9 >=dev-perl/Graph-0.86 dev-lang/perl:= +RESTRICT=test !test? ( test ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Network-1.006900.tar.gz +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe perl-functions c3fca037246e877693badea0df3b0ef8 readme.gentoo-r1 204091a2cde6179cd9d3db26d09412d3 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 perl-module 4e37e1004a0a27e41bb7025c0b974676 +_md5_=6c074e2b53c3e7242c6ed1e352537670 diff --git a/metadata/md5-cache/sci-biology/bioperl-run-1.6.9-r1 b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9-r1 new file mode 100644 index 000000000000..7e73cff826f1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bioperl-run-1.6.9-r1 @@ -0,0 +1,16 @@ +BDEPEND=dev-perl/Module-Build dev-lang/perl test? ( >=virtual/perl-Test-Simple-1 ) +DEFINED_PHASES=compile configure install prepare test +DEPEND=>=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 +DESCRIPTION=Perl wrapper modules for key bioinformatics applications +EAPI=8 +HOMEPAGE=http://www.bioperl.org/ +INHERIT=perl-module +IUSE=minimal test 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:= +RESTRICT=test !test? ( test ) +SLOT=0 +SRC_URI=mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe perl-functions c3fca037246e877693badea0df3b0ef8 readme.gentoo-r1 204091a2cde6179cd9d3db26d09412d3 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 perl-module 4e37e1004a0a27e41bb7025c0b974676 +_md5_=517668f69988f82c6a81d26d36633342 diff --git a/metadata/md5-cache/sci-biology/biopython-1.81-r1 b/metadata/md5-cache/sci-biology/biopython-1.81-r1 new file mode 100644 index 000000000000..c4e86d177501 --- /dev/null +++ b/metadata/md5-cache/sci-biology/biopython-1.81-r1 @@ -0,0 +1,16 @@ +BDEPEND=sys-devel/flex python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) >=dev-python/gpep517-15[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/setuptools-67.8.0-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] +DEFINED_PHASES=compile configure install postinst prepare test +DEPEND=dev-python/matplotlib[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/networkx[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/rdflib[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pygraphviz[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/reportlab-3.5.13-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pydot[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 ) +DESCRIPTION=Python modules for computational molecular biology +EAPI=8 +HOMEPAGE=https://www.biopython.org/ https://pypi.org/project/biopython/ +INHERIT=distutils-r1 optfeature pypi +IUSE=python_targets_python3_10 python_targets_python3_11 debug +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=HPND +RDEPEND=dev-python/matplotlib[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/networkx[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/numpy[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/rdflib[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pygraphviz[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-python/reportlab-3.5.13-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/pydot[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 ) +REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 ) +SLOT=0 +SRC_URI=https://files.pythonhosted.org/packages/source/b/biopython/biopython-1.81.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc out-of-source-utils 1a9007554652a6e627edbccb3c25a439 multibuild 30dbf3c5a31db09a19f31ad0a68f2405 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f distutils-r1 d05609532b134be7c4ae2514f4c7d06e optfeature 222cb475c5a4f7ae7cfb0bf510a6fe54 pypi 2eecb475512bc76e5ea9192a681b9e6b +_md5_=8a03119f9fac05f570005f3d1be8aa57 diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1-r2 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2 new file mode 100644 index 000000000000..3cb02e1ff37b --- /dev/null +++ b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2 @@ -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=8 +HOMEPAGE=https://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=https://biosql.org/DIST/biosql-1.0.1.tar.bz2 +_md5_=cc4726c8c2ff5b7c796abd2a154af22a diff --git a/metadata/md5-cache/sci-biology/blat-34-r3 b/metadata/md5-cache/sci-biology/blat-34-r3 new file mode 100644 index 000000000000..e9a83cbb692f --- /dev/null +++ b/metadata/md5-cache/sci-biology/blat-34-r3 @@ -0,0 +1,12 @@ +BDEPEND=app-arch/unzip +DEFINED_PHASES=compile install +DESCRIPTION=The BLAST-Like Alignment Tool, a fast genomic sequence aligner +EAPI=8 +HOMEPAGE=http://www.cse.ucsc.edu/~kent/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=blat +SLOT=0 +SRC_URI=http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=5de19b6facdbdd7214fad082a7d27f77 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.4.4 b/metadata/md5-cache/sci-biology/bowtie-2.4.4 new file mode 100644 index 000000000000..e3cce875ffc5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-2.4.4 @@ -0,0 +1,16 @@ +BDEPEND=app-arch/unzip +DEFINED_PHASES=compile install setup +DEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) dev-lang/perl sys-libs/zlib +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=8 +HOMEPAGE=http://bowtie-bio.sourceforge.net/bowtie2/ +INHERIT=python-single-r1 toolchain-funcs +IUSE=cpu_flags_x86_sse2 examples +python_single_target_python3_10 +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) dev-lang/perl sys-libs/zlib +REQUIRED_USE=cpu_flags_x86_sse2 ^^ ( python_single_target_python3_10 ) +SLOT=2 +SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.4.4/bowtie2-2.4.4-source.zip +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-single-r1 75118e916668a74c660a13b0ecb22562 +_md5_=7e782380091eb080dc11ed573335cbf2 diff --git a/metadata/md5-cache/sci-biology/bowtie-2.5.1 b/metadata/md5-cache/sci-biology/bowtie-2.5.1 new file mode 100644 index 000000000000..ec6368e0b4ea --- /dev/null +++ b/metadata/md5-cache/sci-biology/bowtie-2.5.1 @@ -0,0 +1,17 @@ +BDEPEND=app-arch/unzip test? ( dev-perl/App-cpanminus dev-perl/B-COW dev-perl/Clone dev-perl/Config-General dev-perl/File-Which dev-perl/local-lib dev-perl/Math-Random dev-perl/Test-Deep dev-perl/Text-Template ) +DEFINED_PHASES=compile install setup +DEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) dev-lang/perl sys-libs/zlib +DESCRIPTION=Popular short read aligner for Next-generation sequencing data +EAPI=8 +HOMEPAGE=https://bowtie-bio.sourceforge.net/bowtie2/ +INHERIT=python-single-r1 toolchain-funcs +IUSE=test cpu_flags_x86_sse2 examples python_single_target_python3_10 python_single_target_python3_11 +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) dev-lang/perl sys-libs/zlib +REQUIRED_USE=cpu_flags_x86_sse2 ^^ ( python_single_target_python3_10 python_single_target_python3_11 ) +RESTRICT=test +SLOT=2 +SRC_URI=mirror://sourceforge/project/bowtie-bio/bowtie2/2.5.1/bowtie2-2.5.1-source.zip +_eclasses_=multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-single-r1 75118e916668a74c660a13b0ecb22562 +_md5_=831933c38b43e507442ee567a3c3583f diff --git a/metadata/md5-cache/sci-biology/bwa-0.7.17 b/metadata/md5-cache/sci-biology/bwa-0.7.17 new file mode 100644 index 000000000000..365412c330fa --- /dev/null +++ b/metadata/md5-cache/sci-biology/bwa-0.7.17 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install +DEPEND=sys-libs/zlib +DESCRIPTION=Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner +EAPI=7 +HOMEPAGE=https://github.com/lh3/bwa/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 ~x64-macos +LICENSE=GPL-3 +RDEPEND=sys-libs/zlib dev-lang/perl +SLOT=0 +SRC_URI=https://github.com/lh3/bwa/archive/v0.7.17.tar.gz -> bwa-0.7.17.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=620c3569e8293303737f7844385c7e82 diff --git a/metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 b/metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 new file mode 100644 index 000000000000..d54bfd408160 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cd-hit-4.6.6-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install pretend setup +DESCRIPTION=Clustering Database at High Identity with Tolerance +EAPI=8 +HOMEPAGE=http://weizhong-lab.ucsd.edu/cd-hit/ +INHERIT=toolchain-funcs +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=72c254d2d4b43c49ff9b0ddcde699acb diff --git a/metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 new file mode 100644 index 000000000000..525b37aa3e22 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustal-omega-1.2.4-r1 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=install prepare +DEPEND=dev-libs/argtable +DESCRIPTION=Scalable multiple alignment of protein sequences +EAPI=8 +HOMEPAGE=http://www.clustal.org/omega/ +INHERIT=autotools +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_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=e2928c88a8676586ff3c5e4a7f534608 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..9e9b52f44ab0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-1.83-r4 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install prepare +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=8 +HOMEPAGE=http://www.embl-heidelberg.de/~seqanal/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~ppc ppc64 sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=clustalw +SLOT=1 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.UNIX.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=48325a27354b2683cb1b693a641b7ab7 diff --git a/metadata/md5-cache/sci-biology/clustalw-2.1-r2 b/metadata/md5-cache/sci-biology/clustalw-2.1-r2 new file mode 100644 index 000000000000..292b56715d8b --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-2.1-r2 @@ -0,0 +1,9 @@ +DEFINED_PHASES=install +DESCRIPTION=General purpose multiple alignment program for DNA and proteins +EAPI=8 +HOMEPAGE=http://www.clustal.org/ +KEYWORDS=amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-3 LGPL-3 +SLOT=2 +SRC_URI=http://www.clustal.org/download/current/clustalw-2.1.tar.gz +_md5_=f31e34b6f62eb36c64c11cb4ad763a55 diff --git a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r3 b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r3 new file mode 100644 index 000000000000..d9f548d576a1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r3 @@ -0,0 +1,14 @@ +DEFINED_PHASES=install prepare +DEPEND=virtual/mpi +DESCRIPTION=An MPI implemention of the ClustalW general purpose multiple alignment algorithm +EAPI=7 +HOMEPAGE=http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php +INHERIT=toolchain-funcs +IUSE=mpi-njtree static-pairalign +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=virtual/mpi +SLOT=0 +SRC_URI=http://web.bii.a-star.edu.sg/~kuobin/clustalw-mpi/clustalw-mpi-0.13.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=689841db0e3b7d6629b51049a2942165 diff --git a/metadata/md5-cache/sci-biology/clustalx-2.1-r3 b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 new file mode 100644 index 000000000000..e60ca2f9b8b3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/clustalx-2.1-r3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install prepare +DEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 +DESCRIPTION=Graphical interface for the ClustalW multiple alignment program +EAPI=7 +HOMEPAGE=https://www.ebi.ac.uk/Tools/msa/clustalw2/ +INHERIT=desktop qmake-utils +KEYWORDS=amd64 ~x86 +LICENSE=GPL-3 LGPL-3 +RDEPEND=dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 dev-qt/qtxml:5 >=sci-biology/clustalw-2.1 +SLOT=0 +SRC_URI=http://www.clustal.org/download/current/clustalx-2.1.tar.gz https://dev.gentoo.org/~jlec/distfiles/clustalx.png.xz +_eclasses_=desktop 021728fdc1b03b36357dbc89489e0f0d toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 qmake-utils a8dd17b1d94586164f5e3fc12b1c6b81 +_md5_=26ebb7c606a394252d2be9f3c156984f diff --git a/metadata/md5-cache/sci-biology/cutg-160-r1 b/metadata/md5-cache/sci-biology/cutg-160-r1 new file mode 100644 index 000000000000..439eebf601f7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/cutg-160-r1 @@ -0,0 +1,13 @@ +BDEPEND=emboss? ( sci-biology/emboss ) +DEFINED_PHASES=compile install +DESCRIPTION=Codon usage tables calculated from GenBank +EAPI=7 +HOMEPAGE=http://www.kazusa.or.jp/codon/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/cutg-160.tar.xz +_md5_=f85abfb1030988c2814b5f00d0d171b0 diff --git a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 new file mode 100644 index 000000000000..ea3a7ff2bd9a --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install postinst +DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment +EAPI=7 +HOMEPAGE=http://dialign-tx.gobics.de/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=b2a78c4cfa60eb348ae63d076ecb5fba diff --git a/metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 b/metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 new file mode 100644 index 000000000000..c5c5e2a2eb00 --- /dev/null +++ b/metadata/md5-cache/sci-biology/dialign2-2.2.1-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Multiple sequence alignment +EAPI=8 +HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2.1 +SLOT=0 +SRC_URI=http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=879353dc71e4dca1cd8026068a0c808c diff --git a/metadata/md5-cache/sci-biology/elph-1.0.1-r3 b/metadata/md5-cache/sci-biology/elph-1.0.1-r3 new file mode 100644 index 000000000000..1cee387a6536 --- /dev/null +++ b/metadata/md5-cache/sci-biology/elph-1.0.1-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Estimated Locations of Pattern Hits - Motif finder program +EAPI=8 +HOMEPAGE=http://cbcb.umd.edu/software/ELPH/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=33ffc2d8f7374d9619cfcb1838da0680 diff --git a/metadata/md5-cache/sci-biology/embassy-6.6.0-r3 b/metadata/md5-cache/sci-biology/embassy-6.6.0-r3 new file mode 100644 index 000000000000..0e21d758fe16 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-6.6.0-r3 @@ -0,0 +1,9 @@ +DEFINED_PHASES=- +DESCRIPTION=A meta-package for installing all EMBASSY packages (EMBOSS add-ons) +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/embassy/ +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=metapackage +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-mse-3.0.0.660 >=sci-biology/embassy-phylipnew-3.69.660 >=sci-biology/embassy-signature-0.1.660 >=sci-biology/embassy-structure-0.1.660 >=sci-biology/embassy-topo-2.0.660 >=sci-biology/embassy-vienna-1.7.2.660 +SLOT=0 +_md5_=333771824b2ddf2c69b9e8dbf988bfd9 diff --git a/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660-r1 b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660-r1 new file mode 100644 index 000000000000..b98ca68d82e3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-cbstools-1.0.0.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Applications from the CBS group +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.660.tar.gz -> embassy-cbstools-1.0.0.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=56469e1c3bb7c4baac8ad99638b59ff0 diff --git a/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660-r1 b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660-r1 new file mode 100644 index 000000000000..71d92015e1e3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-clustalomega-1.1.0.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/clustal-omega dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-1.1.0.660.tar.gz -> embassy-clustalomega-1.1.0.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=864a13621791118f794da4601dcde749 diff --git a/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660-r1 b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660-r1 new file mode 100644 index 000000000000..885acdb4faa9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domainatrix-0.1.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain analysis add-on package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.660.tar.gz -> embassy-domainatrix-0.1.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=af29c98cab7134ba05c6d874e37d95dc diff --git a/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660-r1 b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660-r1 new file mode 100644 index 000000000000..28e5c05ac0ab --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domalign-0.1.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain alignment add-on package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.660.tar.gz -> embassy-domalign-0.1.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=677a5e171c80e94969c1ab9c0b55e283 diff --git a/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660-r1 b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660-r1 new file mode 100644 index 000000000000..0feb4f998444 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-domsearch-0.1.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Protein domain search add-on package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.660.tar.gz -> embassy-domsearch-0.1.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=e0ca10c2776835b0cd20c1b0f0721a1a diff --git a/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660-r1 b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660-r1 new file mode 100644 index 000000000000..9a7071b39bb6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-emnu-1.05.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=sys-libs/ncurses:0= dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Simple menu of EMBOSS applications +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sys-libs/ncurses:0= dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.660.tar.gz -> embassy-emnu-1.05.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=a33d45b5be798e7ebfcef8c59a300c88 diff --git a/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660-r1 b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660-r1 new file mode 100644 index 000000000000..647037ddeed9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-esim4-1.0.0.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.660.tar.gz -> embassy-esim4-1.0.0.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=95026ca22c2bacedf52a70b4428e7753 diff --git a/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660-r1 b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660-r1 new file mode 100644 index 000000000000..8746b7867e64 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-hmmer-2.3.2.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sci-biology/hmmer:2 dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.660.tar.gz -> embassy-hmmer-2.3.2.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=fb64fb071ec661ab550e0b33bc78b536 diff --git a/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660-r1 b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660-r1 new file mode 100644 index 000000000000..5da6d3e7dbb0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-iprscan-4.3.1.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of InterProScan motif detection add-on package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.660.tar.gz -> embassy-iprscan-4.3.1.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=06b3cb4ecb53ada6b96c0f8fe91680e9 diff --git a/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660-r1 b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660-r1 new file mode 100644 index 000000000000..f22673ed80dd --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-mse-3.0.0.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=sys-libs/ncurses:= dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of MSE - Multiple Sequence Screen Editor +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=sys-libs/ncurses:= dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.660.tar.gz -> embassy-mse-3.0.0.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=b6d66fbfe89f6c64f635551357dc90f4 diff --git a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660-r1 b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660-r1 new file mode 100644 index 000000000000..b96efeb23a06 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of The Phylogeny Inference Package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 free-noncomm +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.660.tar.gz -> embassy-phylipnew-3.69.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=93c762366f9cfe8fbfdffd0fdc0483d5 diff --git a/metadata/md5-cache/sci-biology/embassy-signature-0.1.660-r1 b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660-r1 new file mode 100644 index 000000000000..710c49d90026 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-signature-0.1.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Protein signature add-on package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.660.tar.gz -> embassy-signature-0.1.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=193e23282bfd7f7751d7e37988a0ec44 diff --git a/metadata/md5-cache/sci-biology/embassy-structure-0.1.660-r1 b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660-r1 new file mode 100644 index 000000000000..fa3c1d67e013 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-structure-0.1.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Protein structure add-on package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.660.tar.gz -> embassy-structure-0.1.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=c54138383c80476f9d515e5e2a33acaf diff --git a/metadata/md5-cache/sci-biology/embassy-topo-2.0.660-r1 b/metadata/md5-cache/sci-biology/embassy-topo-2.0.660-r1 new file mode 100644 index 000000000000..a7557a69e908 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-topo-2.0.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Transmembrane protein display +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.660.tar.gz -> embassy-topo-2.0.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=30ddf1c7471e11d692477ffa5a3a9956 diff --git a/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660-r1 b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660-r1 new file mode 100644 index 000000000000..b752758de3e9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/embassy-vienna-1.7.2.660-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +DESCRIPTION=EMBOSS integrated version of Vienna RNA package - RNA folding +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 +IUSE=mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 +RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) >=sci-biology/emboss-6.6.0-r1[mysql=,pdf=,png=,postgres=,X=] +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.660.tar.gz -> embassy-vienna-1.7.2.660.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a +_md5_=ba0cdfe4fa4ef35b15cb45a53f81f3b7 diff --git a/metadata/md5-cache/sci-biology/emboss-6.6.0-r2 b/metadata/md5-cache/sci-biology/emboss-6.6.0-r2 new file mode 100644 index 000000000000..1bf534d527ef --- /dev/null +++ b/metadata/md5-cache/sci-biology/emboss-6.6.0-r2 @@ -0,0 +1,16 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install postinst prepare +DEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +DESCRIPTION=The European Molecular Biology Open Software Suite - A sequence analysis package +EAPI=8 +HOMEPAGE=http://emboss.sourceforge.net/ +INHERIT=autotools emboss-r3 readme.gentoo-r1 +IUSE=minimal mysql pdf png postgres X +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0 +PDEPEND=!minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/primer3 sci-biology/prints sci-biology/prosite sci-biology/rebase ) +RDEPEND=!games-action/xbomber !sys-devel/cons dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql? ( dev-db/mysql-connector-c:0= ) pdf? ( media-libs/libharu:= ) png? ( media-libs/gd:2=[png] ) postgres? ( dev-db/postgresql:= ) X? ( x11-libs/libXt ) +SLOT=0 +SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz https://dev.gentoo.org/~soap/distfiles/emboss-6.6.0-patches-r1.tar.xz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc emboss-r3 ed4c0b270092039c992b771a26ca322a readme.gentoo-r1 204091a2cde6179cd9d3db26d09412d3 +_md5_=9856dbbe227d34ba8fd5a46c30dc912f diff --git a/metadata/md5-cache/sci-biology/eugene-4.1d-r1 b/metadata/md5-cache/sci-biology/eugene-4.1d-r1 new file mode 100644 index 000000000000..93bd0feb61c8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/eugene-4.1d-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=prepare +DEPEND=media-libs/gd[png] media-libs/libpng:= +DESCRIPTION=Prokaryotic and Eukaryotic gene predictor +EAPI=8 +HOMEPAGE=http://eugene.toulouse.inra.fr/ +INHERIT=autotools +KEYWORDS=amd64 ~x86 +LICENSE=Artistic +RDEPEND=media-libs/gd[png] media-libs/libpng:= +RESTRICT=test +SLOT=0 +SRC_URI=https://mulcyber.toulouse.inra.fr/frs/download.php/1359/eugene-4.1d.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=88a096386941104cea7615974ecef526 diff --git a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 new file mode 100644 index 000000000000..32db80917e6b --- /dev/null +++ b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 @@ -0,0 +1,17 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=dev-libs/glib:2 +DESCRIPTION=Generic tool for pairwise sequence comparison +EAPI=8 +HOMEPAGE=https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate +INHERIT=autotools toolchain-funcs +IUSE=test utils +KEYWORDS=~amd64 ~x86 ~ppc-macos ~x64-macos +LICENSE=GPL-3 +RDEPEND=dev-libs/glib:2 +REQUIRED_USE=test? ( utils ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=4bd132dac9c502e76b3000e9c6d1e897 diff --git a/metadata/md5-cache/sci-biology/fasta-36.3.8h-r1 b/metadata/md5-cache/sci-biology/fasta-36.3.8h-r1 new file mode 100644 index 000000000000..75827157222c --- /dev/null +++ b/metadata/md5-cache/sci-biology/fasta-36.3.8h-r1 @@ -0,0 +1,14 @@ +BDEPEND=test? ( app-shells/tcsh ) +DEFINED_PHASES=compile install prepare test +DESCRIPTION=FASTA is a DNA and Protein sequence alignment software package +EAPI=8 +HOMEPAGE=https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml +INHERIT=flag-o-matic toolchain-funcs +IUSE=debug cpu_flags_x86_sse2 test +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=fasta +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/wrpearson/fasta36/archive/refs/tags/v36.3.8h_04-May-2020.tar.gz -> fasta-36.3.8h.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=741f3be1a17b816aabab39443236f37b diff --git a/metadata/md5-cache/sci-biology/fasttree-2.1.11 b/metadata/md5-cache/sci-biology/fasttree-2.1.11 new file mode 100644 index 000000000000..9635166d3ead --- /dev/null +++ b/metadata/md5-cache/sci-biology/fasttree-2.1.11 @@ -0,0 +1,14 @@ +BDEPEND=>=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 +DEFINED_PHASES=compile configure install prepare test unpack +DESCRIPTION=Fast inference of approximately-maximum-likelihood phylogenetic trees +EAPI=7 +HOMEPAGE=http://www.microbesonline.org/fasttree/ +INHERIT=cmake +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-2.1.11.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.11.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.11.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 xdg-utils baea6080dd821f5562d715887954c9d3 cmake fc2f89084f590ac95c004ea95b0d2f80 +_md5_=4a94b8db43f0aadb5ece67757ccbe635 diff --git a/metadata/md5-cache/sci-biology/fastx_toolkit-0.0.14-r1 b/metadata/md5-cache/sci-biology/fastx_toolkit-0.0.14-r1 new file mode 100644 index 000000000000..2a871389baa8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/fastx_toolkit-0.0.14-r1 @@ -0,0 +1,14 @@ +BDEPEND=virtual/pkgconfig sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=prepare +DEPEND=sci-biology/libgtextutils:= +DESCRIPTION=Tools for Short Read FASTA/FASTQ file processing +EAPI=8 +HOMEPAGE=http://hannonlab.cshl.edu/fastx_toolkit +INHERIT=autotools +KEYWORDS=~amd64 ~x86 +LICENSE=AGPL-3 +RDEPEND=sci-biology/libgtextutils:= dev-perl/PerlIO-gzip dev-perl/GDGraph sci-visualization/gnuplot +SLOT=0 +SRC_URI=https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=e0ed8e935eca944dc874fee38c4435ad diff --git a/metadata/md5-cache/sci-biology/finchtv-1.3.1-r3 b/metadata/md5-cache/sci-biology/finchtv-1.3.1-r3 new file mode 100644 index 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+HOMEPAGE=https://foldingathome.org/ +INHERIT=systemd +KEYWORDS=~amd64 +LICENSE=FAH-EULA-2014 FAH-special-permission +RDEPEND=acct-group/foldingathome acct-group/video acct-user/foldingathome app-arch/bzip2 || ( dev-libs/openssl-compat:1.0.0 =dev-libs/openssl-1.0*:* ) sys-devel/gcc sys-libs/glibc sys-libs/zlib +RESTRICT=mirror bindist strip +SLOT=0 +SRC_URI=https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v7.6/fahclient_7.6.13-64bit-release.tar.bz2 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 systemd c8b03e8df84486aa991d4396686e8942 +_md5_=f2ef46b617dbd53a6e9dbdd86ff70bf1 diff --git a/metadata/md5-cache/sci-biology/foldingathome-7.6.21 b/metadata/md5-cache/sci-biology/foldingathome-7.6.21 new file mode 100644 index 000000000000..16ca08921f8e --- /dev/null +++ b/metadata/md5-cache/sci-biology/foldingathome-7.6.21 @@ -0,0 +1,15 @@ +BDEPEND=virtual/pkgconfig +DEFINED_PHASES=config install postinst postrm setup +DEPEND=dev-util/patchelf +DESCRIPTION=Folding@Home is a distributed computing project for protein folding +EAPI=8 +HOMEPAGE=https://foldingathome.org/ +INHERIT=systemd +KEYWORDS=~amd64 +LICENSE=FAH-EULA-2014 FAH-special-permission +RDEPEND=acct-group/foldingathome acct-group/video acct-user/foldingathome app-arch/bzip2 || ( dev-libs/openssl-compat:1.0.0 =dev-libs/openssl-1.0*:* ) sys-devel/gcc sys-libs/glibc sys-libs/zlib +RESTRICT=mirror bindist strip +SLOT=0 +SRC_URI=https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v7.6/fahclient_7.6.21-64bit-release.tar.bz2 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 systemd c8b03e8df84486aa991d4396686e8942 +_md5_=50de4ff6faf3b5ac3ed140d8e1653c23 diff --git a/metadata/md5-cache/sci-biology/glimmer-3.02b b/metadata/md5-cache/sci-biology/glimmer-3.02b new file mode 100644 index 000000000000..21888f3a0a6e --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmer-3.02b @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=An HMM-based microbial gene finding system from TIGR +EAPI=7 +HOMEPAGE=https://ccb.jhu.edu/software/glimmer/index.shtml +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=Artistic +RDEPEND=app-shells/tcsh sci-biology/elph +SLOT=0 +SRC_URI=https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=a7e8ed9c8bc30ed68f4fc465709c2e3d diff --git a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 new file mode 100644 index 000000000000..53a27bedccbb --- /dev/null +++ b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=A eukaryotic gene finding system from TIGR +EAPI=7 +HOMEPAGE=http://www.cbcb.umd.edu/software/GlimmerHMM/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~x86 +LICENSE=Artistic +SLOT=0 +SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.1.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=7e23482cbed8382298f1fb42831ae018 diff --git a/metadata/md5-cache/sci-biology/gmap-2020.10.27 b/metadata/md5-cache/sci-biology/gmap-2020.10.27 new file mode 100644 index 000000000000..487916a59aeb --- /dev/null +++ b/metadata/md5-cache/sci-biology/gmap-2020.10.27 @@ -0,0 +1,9 @@ +DEFINED_PHASES=- +DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences +EAPI=7 +HOMEPAGE=http://research-pub.gene.com/gmap/ +KEYWORDS=~amd64 ~x86 +LICENSE=gmap +SLOT=0 +SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2020-10-27.tar.gz +_md5_=9c28013ebc925bd0d07b8a1b1f1dbc4d diff --git a/metadata/md5-cache/sci-biology/hmmer-2.3.2-r5 b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r5 new file mode 100644 index 000000000000..95f8805d5ad6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-2.3.2-r5 @@ -0,0 +1,14 @@ +BDEPEND=test? ( dev-lang/perl ) +DEFINED_PHASES=compile configure install postinst +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=8 +HOMEPAGE=http://hmmer.org/ +INHERIT=flag-o-matic toolchain-funcs +IUSE=cpu_flags_ppc_altivec test +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RESTRICT=!test? ( test ) +SLOT=2 +SRC_URI=http://eddylab.org/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=766670f9df1a2a937b1b58cf4c63931d diff --git a/metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1 b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1 new file mode 100644 index 000000000000..474db9ee75c4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/hmmer-3.1_beta2-r1 @@ -0,0 +1,16 @@ +BDEPEND=test? ( dev-lang/perl ) +DEFINED_PHASES=compile configure install +DEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) +DESCRIPTION=Sequence analysis using profile hidden Markov models +EAPI=8 +HOMEPAGE=http://hmmer.org/ +INHERIT=toolchain-funcs +IUSE=cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=66609c69302596b8671531f5be5cf6c1 diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r2 b/metadata/md5-cache/sci-biology/iedera-1.05-r2 new file mode 100644 index 000000000000..7b6f7bebc7be --- /dev/null +++ b/metadata/md5-cache/sci-biology/iedera-1.05-r2 @@ -0,0 +1,12 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=prepare +DESCRIPTION=Subset seed design tool for DNA sequence alignment +EAPI=8 +HOMEPAGE=https://bioinfo.lifl.fr/yass/iedera.php +INHERIT=autotools +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=c1df71458cdeda01ad17b744ef31dc36 diff --git a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 new file mode 100644 index 000000000000..a59b74c6b7ab --- /dev/null +++ b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 @@ -0,0 +1,14 @@ +DEFINED_PHASES=configure install +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Inference of RNA alignments +EAPI=7 +HOMEPAGE=http://infernal.janelia.org/ +INHERIT=toolchain-funcs +IUSE=mpi +KEYWORDS=amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=mpi? ( virtual/mpi ) +SLOT=0 +SRC_URI=ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=ed6542a9fbe6d76d42075ee482329775 diff --git a/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2 b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2 new file mode 100644 index 000000000000..c7959fab6eed --- /dev/null +++ b/metadata/md5-cache/sci-biology/iqpnni-3.3.2-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=Important Quartet Puzzling and NNI Operation +EAPI=8 +HOMEPAGE=http://www.cibiv.at/software/iqpnni/ +IUSE=doc +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.cibiv.at/software/iqpnni/iqpnni-3.3.2.tar.gz +_md5_=6aae6556c487f2f133af3a40ec0d227b diff --git a/metadata/md5-cache/sci-biology/kalign-2.03-r3 b/metadata/md5-cache/sci-biology/kalign-2.03-r3 new file mode 100644 index 000000000000..1c563dbab5c8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/kalign-2.03-r3 @@ -0,0 +1,9 @@ +DEFINED_PHASES=- +DESCRIPTION=Global and progressive multiple sequence alignment +EAPI=8 +HOMEPAGE=http://msa.cgb.ki.se/ +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://debian/pool/main/k/kalign/kalign_2.03.orig.tar.gz +_md5_=6f3350a7a60bf9efddc24e958998f592 diff --git a/metadata/md5-cache/sci-biology/kallisto-0.46.2 b/metadata/md5-cache/sci-biology/kallisto-0.46.2 new file mode 100644 index 000000000000..b803b991eb79 --- /dev/null +++ b/metadata/md5-cache/sci-biology/kallisto-0.46.2 @@ -0,0 +1,16 @@ +BDEPEND=virtual/pkgconfig >=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 +DEFINED_PHASES=compile configure install prepare test +DEPEND=sci-libs/htslib:= sys-libs/zlib:= hdf5? ( sci-libs/hdf5:= ) test? ( dev-cpp/catch:0 sci-libs/hdf5 ) +DESCRIPTION=Near-optimal RNA-Seq quantification +EAPI=7 +HOMEPAGE=http://pachterlab.github.io/kallisto/ +INHERIT=cmake +IUSE=hdf5 test +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=BSD +RDEPEND=sci-libs/htslib:= sys-libs/zlib:= hdf5? ( sci-libs/hdf5:= ) +RESTRICT=!test? ( test ) +SLOT=0 +SRC_URI=https://github.com/pachterlab/kallisto/archive/v0.46.2.tar.gz -> kallisto-0.46.2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 xdg-utils baea6080dd821f5562d715887954c9d3 cmake fc2f89084f590ac95c004ea95b0d2f80 +_md5_=1b739cad0275e6dc5a320723611b78e9 diff --git a/metadata/md5-cache/sci-biology/lagan-2.0-r4 b/metadata/md5-cache/sci-biology/lagan-2.0-r4 new file mode 100644 index 000000000000..a4a5ac6decec --- /dev/null +++ b/metadata/md5-cache/sci-biology/lagan-2.0-r4 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install prepare +DESCRIPTION=The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA +EAPI=7 +HOMEPAGE=http://lagan.stanford.edu/lagan_web/index.shtml +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl +SLOT=0 +SRC_URI=http://lagan.stanford.edu/lagan_web/lagan20.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=c4b4e347541c85d423cac28e03a104d4 diff --git a/metadata/md5-cache/sci-biology/libgtextutils-0.6.1-r1 b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1-r1 new file mode 100644 index 000000000000..fc70f5b47758 --- /dev/null +++ b/metadata/md5-cache/sci-biology/libgtextutils-0.6.1-r1 @@ -0,0 +1,12 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=install prepare +DESCRIPTION=Gordon Text utils Library +EAPI=8 +HOMEPAGE=http://hannonlab.cshl.edu/fastx_toolkit/ +INHERIT=autotools +KEYWORDS=~amd64 ~x86 +LICENSE=AGPL-3 +SLOT=0/0 +SRC_URI=http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.1.tar.bz2 +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=bf69c3370f31858d1ff072c30305ca99 diff --git a/metadata/md5-cache/sci-biology/mafft-7.490 b/metadata/md5-cache/sci-biology/mafft-7.490 new file mode 100644 index 000000000000..98d9d05f87db --- /dev/null +++ b/metadata/md5-cache/sci-biology/mafft-7.490 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install prepare test +DESCRIPTION=Multiple sequence alignments using a variety of algorithms +EAPI=8 +HOMEPAGE=https://mafft.cbrc.jp/alignment/software/index.html +INHERIT=flag-o-matic toolchain-funcs +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos +LICENSE=BSD +SLOT=0 +SRC_URI=https://mafft.cbrc.jp/alignment/software/mafft-7.490-without-extensions-src.tgz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=04971be2bc4044a9c136d12a7e51b23d diff --git a/metadata/md5-cache/sci-biology/maq-0.7.1-r3 b/metadata/md5-cache/sci-biology/maq-0.7.1-r3 new file mode 100644 index 000000000000..363360791be3 --- /dev/null +++ b/metadata/md5-cache/sci-biology/maq-0.7.1-r3 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=install prepare +DEPEND=sys-libs/zlib +DESCRIPTION=Mapping and Assembly with Qualities, mapping NGS reads to reference genomes +EAPI=8 +HOMEPAGE=http://maq.sourceforge.net/ +INHERIT=autotools +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-3 +RDEPEND=sys-libs/zlib +SLOT=0 +SRC_URI=mirror://sourceforge/maq/maq-0.7.1.tar.bz2 mirror://sourceforge/maq/calib-36.dat.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=063e8f4add19e5b685018dfb11be0196 diff --git a/metadata/md5-cache/sci-biology/maqview-0.2.5-r4 b/metadata/md5-cache/sci-biology/maqview-0.2.5-r4 new file mode 100644 index 000000000000..557127f085ee --- /dev/null +++ b/metadata/md5-cache/sci-biology/maqview-0.2.5-r4 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=prepare +DEPEND=media-libs/freeglut sys-libs/zlib +DESCRIPTION=GUI for sci-biology/maq, a short read mapping assembler +EAPI=8 +HOMEPAGE=http://maq.sourceforge.net/ +INHERIT=autotools +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=media-libs/freeglut sys-libs/zlib sci-biology/maq +SLOT=0 +SRC_URI=mirror://sourceforge/maq/maqview-0.2.5.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=ce6e22a8dca500f24263e27d73b9eda4 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..50ee556598dc --- /dev/null +++ b/metadata/md5-cache/sci-biology/mcl-14.137 @@ -0,0 +1,13 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure prepare +DESCRIPTION=A Markov Cluster Algorithm implementation +EAPI=7 +HOMEPAGE=http://micans.org/mcl/ +INHERIT=autotools +IUSE=+blast +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://micans.org/mcl/src/mcl-14-137.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=9779366f51f2fea08274072a9a019159 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..83d063b3db50 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mosaik-2.2.30 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install unpack +DESCRIPTION=A reference-guided aligner for next-generation sequencing technologies +EAPI=7 +HOMEPAGE=https://github.com/wanpinglee/MOSAIK +INHERIT=flag-o-matic toolchain-funcs vcs-snapshot +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc vcs-snapshot eab6d8533446763c2e9777d8bbd1594e +_md5_=b275a0e18dbe85d2a2e24cebc796c134 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..9c42bc307593 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mothur-1.27.0-r1 @@ -0,0 +1,15 @@ +BDEPEND=app-arch/unzip virtual/fortran +DEFINED_PHASES=compile configure install setup +DEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran +DESCRIPTION=A suite of algorithms for ecological bioinformatics +EAPI=7 +HOMEPAGE=https://www.mothur.org/ +INHERIT=flag-o-matic fortran-2 toolchain-funcs +IUSE=mpi +readline +KEYWORDS=amd64 ~x86 +LICENSE=GPL-3 +RDEPEND=sci-biology/uchime mpi? ( virtual/mpi ) virtual/fortran +SLOT=0 +SRC_URI=https://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip -> mothur-1.27.0.zip +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc fortran-2 40c4450f1c4ecb2ee694d96e1958d4ea +_md5_=4d1c6c16f8757994256f73d5be45cb8f 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..eec095cb038c --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r2 @@ -0,0 +1,14 @@ +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/ncurses:= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:= ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=8 +HOMEPAGE=http://mrbayes.csit.fsu.edu/ +INHERIT=toolchain-funcs +IUSE=debug mpi readline +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses:= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:= ) +SLOT=0 +SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=90cf0e9cbae92852e8eb4b8ac547c951 diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.2.7 b/metadata/md5-cache/sci-biology/mrbayes-3.2.7 new file mode 100644 index 000000000000..2c3ced1ec774 --- /dev/null +++ b/metadata/md5-cache/sci-biology/mrbayes-3.2.7 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure +DEPEND=sys-libs/ncurses:= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:= ) +DESCRIPTION=Bayesian Inference of Phylogeny +EAPI=8 +HOMEPAGE=https://nbisweden.github.io/MrBayes/ +IUSE=debug mpi readline +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +RDEPEND=sys-libs/ncurses:= mpi? ( virtual/mpi ) readline? ( sys-libs/readline:= ) +REQUIRED_USE=mpi? ( !readline ) +SLOT=0 +SRC_URI=https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz +_md5_=68e9f13e095c1cd32bc206b1331b2bc0 diff --git a/metadata/md5-cache/sci-biology/mummer-3.23-r1 b/metadata/md5-cache/sci-biology/mummer-3.23-r1 new file mode 100644 index 000000000000..4fa644fa068f --- /dev/null +++ b/metadata/md5-cache/sci-biology/mummer-3.23-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A rapid whole genome aligner +EAPI=8 +HOMEPAGE=http://mummer.sourceforge.net/ +INHERIT=flag-o-matic toolchain-funcs +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=7103f6fc8a8d965ba2e5b71b09010e1d 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..cd16f958e61a --- /dev/null +++ b/metadata/md5-cache/sci-biology/muscle-3.8.31 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Multiple sequence comparison by log-expectation +EAPI=7 +HOMEPAGE=https://www.drive5.com/muscle/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~ppc ~x86 +LICENSE=public-domain +RDEPEND=!sci-libs/libmuscle +SLOT=0 +SRC_URI=https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=62859cbc1404e079f9f85e83527914cf diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6-r1 b/metadata/md5-cache/sci-biology/newick-utils-1.6-r1 new file mode 100644 index 000000000000..8bd4cb119c40 --- /dev/null +++ b/metadata/md5-cache/sci-biology/newick-utils-1.6-r1 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure install prepare +DEPEND=xml? ( dev-libs/libxml2 ) +DESCRIPTION=Tools for processing phylogenetic trees +EAPI=7 +HOMEPAGE=http://cegg.unige.ch/newick_utils +INHERIT=autotools +IUSE=xml +KEYWORDS=~amd64 ~x86 +LICENSE=BSD +RDEPEND=xml? ( dev-libs/libxml2 ) !dev-games/libnw +SLOT=0 +SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=fac40fe86b457a75883a5eb465ce18d8 diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r2 b/metadata/md5-cache/sci-biology/pals-1.0-r2 new file mode 100644 index 000000000000..676c6dab82ba --- /dev/null +++ b/metadata/md5-cache/sci-biology/pals-1.0-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Pairwise Aligner for Long Sequences +EAPI=8 +HOMEPAGE=https://www.drive5.com/pals/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=https://www.drive5.com/pals/pals_source.tar.gz -> pals-1.0.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=eacca1433c8023d7321f6b8d4fc4b6d4 diff --git a/metadata/md5-cache/sci-biology/paml-4.9j b/metadata/md5-cache/sci-biology/paml-4.9j new file mode 100644 index 000000000000..b6cbc0aaa736 --- /dev/null +++ b/metadata/md5-cache/sci-biology/paml-4.9j @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=Phylogenetic Analysis by Maximum Likelihood +EAPI=7 +HOMEPAGE=http://abacus.gene.ucl.ac.uk/software/paml.html +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=free-noncomm +SLOT=0 +SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=236ce838eff8e04f8059e18110b3ff38 diff --git a/metadata/md5-cache/sci-biology/phylip-3.698 b/metadata/md5-cache/sci-biology/phylip-3.698 new file mode 100644 index 000000000000..246651264dd5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/phylip-3.698 @@ -0,0 +1,14 @@ +BDEPEND=app-arch/unzip +DEFINED_PHASES=compile configure install prepare +DEPEND=x11-libs/libXaw !dev-lang/elixir x11-base/xorg-proto +DESCRIPTION=The PHYLogeny Inference Package +EAPI=7 +HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html +INHERIT=flag-o-matic toolchain-funcs +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=BSD-2 +RDEPEND=x11-libs/libXaw !dev-lang/elixir +SLOT=0 +SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.698.zip +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=b3a777c086ea4a6cd489efcb5bde7b66 diff --git a/metadata/md5-cache/sci-biology/phyml-2.4.5-r4 b/metadata/md5-cache/sci-biology/phyml-2.4.5-r4 new file mode 100644 index 000000000000..46973884b8fc --- /dev/null +++ b/metadata/md5-cache/sci-biology/phyml-2.4.5-r4 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Estimation of large phylogenies by maximum likelihood +EAPI=8 +HOMEPAGE=http://atgc.lirmm.fr/phyml/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~ppc ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=http://www.lirmm.fr/~guindon/phyml_v2.4.5.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=07b5d0c4fa7ccf9c50fb8bba0dca57c7 diff --git a/metadata/md5-cache/sci-biology/piler-1.0-r2 b/metadata/md5-cache/sci-biology/piler-1.0-r2 new file mode 100644 index 000000000000..61d42c381678 --- /dev/null +++ b/metadata/md5-cache/sci-biology/piler-1.0-r2 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of repetitive DNA found in genome sequences +EAPI=8 +HOMEPAGE=http://www.drive5.com/piler/ +INHERIT=toolchain-funcs +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=5fc094c7ed21adb9be841a3f8cf76801 diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r2 b/metadata/md5-cache/sci-biology/pilercr-1.0-r2 new file mode 100644 index 000000000000..a02e445ff3ab --- /dev/null +++ b/metadata/md5-cache/sci-biology/pilercr-1.0-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) +EAPI=8 +HOMEPAGE=http://www.drive5.com/pilercr/ +INHERIT=toolchain-funcs +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=00fbcbaccb202c9a3276728d356746a2 diff --git a/metadata/md5-cache/sci-biology/pilercr-1.0-r3 b/metadata/md5-cache/sci-biology/pilercr-1.0-r3 new file mode 100644 index 000000000000..2f0e93e8bfa9 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pilercr-1.0-r3 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) +EAPI=8 +HOMEPAGE=https://www.drive5.com/pilercr/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=https://www.drive5.com/pilercr/pilercr1.06.tar.gz -> pilercr-1.0.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=a4758999cbdb4e27100e24cb54470db8 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..551a94778fe6 --- /dev/null +++ b/metadata/md5-cache/sci-biology/plink-1.90_pre140514 @@ -0,0 +1,14 @@ +BDEPEND=app-arch/unzip virtual/pkgconfig +DEFINED_PHASES=compile install prepare +DEPEND=sys-libs/zlib virtual/cblas virtual/lapack +DESCRIPTION=Whole genome association analysis toolset +EAPI=8 +HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ +INHERIT=toolchain-funcs +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=419587bbc06b4b3717534c9c0148238b 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..9bbe64f0fa3b --- /dev/null +++ b/metadata/md5-cache/sci-biology/poa-2-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile configure install postinst +DESCRIPTION=Fast multiple sequence alignments using partial-order graphs +EAPI=7 +HOMEPAGE=http://bioinfo.mbi.ucla.edu/poa/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/poamsa/poaV2.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=903ecfa03b5ccff264e1b75f90e8b664 diff --git a/metadata/md5-cache/sci-biology/prank-140603-r1 b/metadata/md5-cache/sci-biology/prank-140603-r1 new file mode 100644 index 000000000000..cf802ce22b3b --- /dev/null +++ b/metadata/md5-cache/sci-biology/prank-140603-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Probabilistic Alignment Kit +EAPI=8 +HOMEPAGE=http://wasabiapp.org/software/prank/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-3 +SLOT=0 +SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=07f1836dd1c44c4ebf19bb6a59f7141a diff --git a/metadata/md5-cache/sci-biology/primer3-2.3.7-r1 b/metadata/md5-cache/sci-biology/primer3-2.3.7-r1 new file mode 100644 index 000000000000..0aad04986214 --- /dev/null +++ b/metadata/md5-cache/sci-biology/primer3-2.3.7-r1 @@ -0,0 +1,12 @@ +BDEPEND=dev-lang/perl +DEFINED_PHASES=compile configure install prepare test +DESCRIPTION=Primer Design for PCR reactions +EAPI=8 +HOMEPAGE=http://primer3.sourceforge.net/ +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/project/primer3/primer3/2.3.7/primer3-2.3.7.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=7c332f2eee3108c0929cddfad29374e7 diff --git a/metadata/md5-cache/sci-biology/prints-39.0-r2 b/metadata/md5-cache/sci-biology/prints-39.0-r2 new file mode 100644 index 000000000000..23a0ba457da1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prints-39.0-r2 @@ -0,0 +1,12 @@ +BDEPEND=emboss? ( sci-biology/emboss ) +DEFINED_PHASES=compile install +DESCRIPTION=A protein motif fingerprint database +EAPI=8 +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 ) +SLOT=0 +SRC_URI=mirror://gentoo/prints-39.0.tar.bz2 +_md5_=79d0547e585a924037242281d1a5469b 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..4733c7444ca4 --- /dev/null +++ b/metadata/md5-cache/sci-biology/probcons-1.12-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile install postinst +DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences +EAPI=7 +HOMEPAGE=http://probcons.stanford.edu/ +INHERIT=toolchain-funcs +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 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=a0d3d7d9a640d31e0ece26e564b37dda diff --git a/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 b/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 new file mode 100644 index 000000000000..5857f3a80dc8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/prodigal-2.6.3-r1 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure +DESCRIPTION=Prokaryotic Dynamic Programming Genefinding Algorithm +EAPI=8 +HOMEPAGE=http://prodigal.ornl.gov/ +INHERIT=toolchain-funcs +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 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=fbd84f84d9eeda38c197893cf2c079c8 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..64ed32ed3b57 --- /dev/null +++ b/metadata/md5-cache/sci-biology/profphd-1.0.40 @@ -0,0 +1,11 @@ +DEFINED_PHASES=compile install +DEPEND=dev-lang/perl +DESCRIPTION=Secondary structure and solvent accessibility predictor +EAPI=7 +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-1.0.40.tar.xz +_md5_=7dd45e26103f891ba0f31da2c73ec2f0 diff --git a/metadata/md5-cache/sci-biology/prosite-2017.02-r1 b/metadata/md5-cache/sci-biology/prosite-2017.02-r1 new file mode 100644 index 000000000000..cef8da6a920b --- /dev/null +++ b/metadata/md5-cache/sci-biology/prosite-2017.02-r1 @@ -0,0 +1,12 @@ +BDEPEND=emboss? ( sci-biology/emboss ) +DEFINED_PHASES=compile install +DESCRIPTION=A protein families and domains database +EAPI=8 +HOMEPAGE=https://prosite.expasy.org/ +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=swiss-prot +RDEPEND=emboss? ( sci-biology/emboss ) +SLOT=0 +SRC_URI=ftp://ftp.expasy.org/databases/prosite/old_releases/prosite2017_02.tar.bz2 +_md5_=05ff9ed4f5365bf3491e146b89f1aa5a diff --git a/metadata/md5-cache/sci-biology/pysam-0.21.0 b/metadata/md5-cache/sci-biology/pysam-0.21.0 new file mode 100644 index 000000000000..f7d646503cc8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pysam-0.21.0 @@ -0,0 +1,17 @@ +BDEPEND=test? ( =sci-biology/bcftools-1.17* =sci-biology/samtools-1.17* ) test? ( =sci-libs/htslib-1.17*:= >=dev-python/pytest-7.3.1[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-67.8.0-r1[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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc out-of-source-utils 1a9007554652a6e627edbccb3c25a439 multibuild 30dbf3c5a31db09a19f31ad0a68f2405 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f distutils-r1 d05609532b134be7c4ae2514f4c7d06e +_md5_=d2f337ee806641d85739cd55c8698806 diff --git a/metadata/md5-cache/sci-biology/pysam-9999 b/metadata/md5-cache/sci-biology/pysam-9999 new file mode 100644 index 000000000000..a8794057f270 --- /dev/null +++ b/metadata/md5-cache/sci-biology/pysam-9999 @@ -0,0 +1,16 @@ +BDEPEND=test? ( >=sci-biology/bcftools-1.17 >=sci-biology/samtools-1.17 ) test? ( >=sci-libs/htslib-1.17 >=dev-python/pytest-7.3.1[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-67.8.0-r1[python_targets_python3_10(-)?,python_targets_python3_11(-)?] >=dev-vcs/git-1.8.2.1[curl] +DEFINED_PHASES=compile configure install prepare test unpack +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 git-r3 +IUSE=test python_targets_python3_10 python_targets_python3_11 +LICENSE=MIT +PROPERTIES=live +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 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc out-of-source-utils 1a9007554652a6e627edbccb3c25a439 multibuild 30dbf3c5a31db09a19f31ad0a68f2405 multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 python-utils-r1 12aa0037eb004139215ff04894d52b28 python-r1 8a28fa6d3e3bc96ff8a7eff2badbe71f distutils-r1 d05609532b134be7c4ae2514f4c7d06e git-r3 2358a7b20091609e24bd3a83b3ac5991 +_md5_=bcdb07ed2c7ed322810daba181d02da3 diff --git a/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 new file mode 100644 index 000000000000..02c6020cba18 --- /dev/null +++ b/metadata/md5-cache/sci-biology/qrna-2.0.3c-r3 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile configure install prepare +DEPEND=dev-lang/perl sci-biology/hmmer:2 +DESCRIPTION=Prototype ncRNA genefinder +EAPI=7 +HOMEPAGE=http://selab.janelia.org/software.html +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl sci-biology/hmmer:2 +SLOT=0 +SRC_URI=mirror://gentoo/qrna-2.0.3c.tar.bz2 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=fdc52d5355060d858ec78d793dc26d81 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..05083baa2a55 --- /dev/null +++ b/metadata/md5-cache/sci-biology/raxml-7.2.6 @@ -0,0 +1,13 @@ +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=14b77d8b019468c10a65f1358be0d8ae diff --git a/metadata/md5-cache/sci-biology/rebase-1901-r2 b/metadata/md5-cache/sci-biology/rebase-1901-r2 new file mode 100644 index 000000000000..7c82bbc26943 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rebase-1901-r2 @@ -0,0 +1,13 @@ +BDEPEND=emboss? ( sci-biology/emboss ) +DEFINED_PHASES=compile install +DESCRIPTION=A restriction enzyme database +EAPI=8 +HOMEPAGE=http://rebase.neb.com +IUSE=emboss minimal +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=public-domain +RDEPEND=emboss? ( sci-biology/emboss ) +RESTRICT=binchecks strip +SLOT=0 +SRC_URI=https://dev.gentoo.org/~jlec/distfiles/rebase-1901.tar.xz +_md5_=1efd94cdd64a4a9cbb888415c3d62b20 diff --git a/metadata/md5-cache/sci-biology/recon-1.08-r1 b/metadata/md5-cache/sci-biology/recon-1.08-r1 new file mode 100644 index 000000000000..d2c51dd33913 --- /dev/null +++ b/metadata/md5-cache/sci-biology/recon-1.08-r1 @@ -0,0 +1,13 @@ +DEFINED_PHASES=compile install prepare +DESCRIPTION=Automated de novo identification of repeat families from genomic sequences +EAPI=8 +HOMEPAGE=http://www.repeatmasker.org/RepeatModeler.html +INHERIT=toolchain-funcs +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=36772ec3438da03e296e39fc88b347ee diff --git a/metadata/md5-cache/sci-biology/rnaview-20040713-r5 b/metadata/md5-cache/sci-biology/rnaview-20040713-r5 new file mode 100644 index 000000000000..b2c463f7fda1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/rnaview-20040713-r5 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Generates 2D displays of RNA/DNA secondary structures with tertiary interactions +EAPI=8 +HOMEPAGE=http://ndbserver.rutgers.edu/services/download/index.html +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +SLOT=0 +SRC_URI=mirror://gentoo/rnaview-20040713.tar.bz2 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=dd5336243d83138448c13acb7f4d4ba2 diff --git a/metadata/md5-cache/sci-biology/samtools-1.17 b/metadata/md5-cache/sci-biology/samtools-1.17 new file mode 100644 index 000000000000..13802a4c8ba8 --- /dev/null +++ b/metadata/md5-cache/sci-biology/samtools-1.17 @@ -0,0 +1,14 @@ +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_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=d899fa7ac2ab4404dcca131cb83b93ab diff --git a/metadata/md5-cache/sci-biology/seaview-4.6-r1 b/metadata/md5-cache/sci-biology/seaview-4.6-r1 new file mode 100644 index 000000000000..fe3d31efdd16 --- /dev/null +++ b/metadata/md5-cache/sci-biology/seaview-4.6-r1 @@ -0,0 +1,15 @@ +BDEPEND=virtual/pkgconfig +DEFINED_PHASES=install prepare +DEPEND=sci-biology/clustalw:2 sci-biology/phyml || ( sci-libs/libmuscle sci-biology/muscle ) sys-libs/zlib x11-libs/fltk:1[xft?] x11-libs/libX11 xft? ( x11-libs/libXft ) +DESCRIPTION=A graphical multiple sequence alignment editor +EAPI=7 +HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html +INHERIT=desktop toolchain-funcs +IUSE=+xft +KEYWORDS=~amd64 ~x86 +LICENSE=public-domain +RDEPEND=sci-biology/clustalw:2 sci-biology/phyml || ( sci-libs/libmuscle sci-biology/muscle ) sys-libs/zlib x11-libs/fltk:1[xft?] x11-libs/libX11 xft? ( x11-libs/libXft ) +SLOT=0 +SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.6.tar.gz +_eclasses_=desktop 021728fdc1b03b36357dbc89489e0f0d toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=a742711d8523a4e49524662c12d647c2 diff --git a/metadata/md5-cache/sci-biology/seqan-3.1.0 b/metadata/md5-cache/sci-biology/seqan-3.1.0 new file mode 100644 index 000000000000..754b5a91de6b --- /dev/null +++ b/metadata/md5-cache/sci-biology/seqan-3.1.0 @@ -0,0 +1,16 @@ +BDEPEND=>=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 +DEFINED_PHASES=compile configure install prepare test +DEPEND=app-arch/bzip2:= dev-cpp/range-v3 dev-libs/cereal sci-libs/lemon sys-libs/zlib:= +DESCRIPTION=C++ Sequence Analysis Library +EAPI=8 +HOMEPAGE=https://www.seqan.de/ +INHERIT=cmake +IUSE=cpu_flags_x86_sse4_2 +KEYWORDS=~amd64 ~x86 ~amd64-linux +LICENSE=BSD GPL-3 +RDEPEND=app-arch/bzip2:= dev-cpp/range-v3 dev-libs/cereal sci-libs/lemon sys-libs/zlib:= +REQUIRED_USE=cpu_flags_x86_sse4_2 +SLOT=0 +SRC_URI=https://github.com/seqan/seqan3/releases/download/3.1.0/seqan3-3.1.0-Source.tar.xz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 xdg-utils baea6080dd821f5562d715887954c9d3 cmake fc2f89084f590ac95c004ea95b0d2f80 +_md5_=327a33751512d78b13d5acd641ba3385 diff --git a/metadata/md5-cache/sci-biology/sibsim4-0.20 b/metadata/md5-cache/sci-biology/sibsim4-0.20 new file mode 100644 index 000000000000..f5cd52767420 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sibsim4-0.20 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A rewrite and improvement upon sim4, a DNA-mRNA aligner +EAPI=7 +HOMEPAGE=http://sibsim4.sourceforge.net/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://sourceforge/sibsim4/SIBsim4-0.20.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=c9dc1d70a172b8258f2f0e4f3f7e967c diff --git a/metadata/md5-cache/sci-biology/sim4-20030921-r2 b/metadata/md5-cache/sci-biology/sim4-20030921-r2 new file mode 100644 index 000000000000..6a6ccc3a0bb0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/sim4-20030921-r2 @@ -0,0 +1,11 @@ +DEFINED_PHASES=configure install +DESCRIPTION=A program to align cDNA and genomic DNA +EAPI=7 +HOMEPAGE=http://globin.cse.psu.edu/html/docs/sim4.html +INHERIT=toolchain-funcs +KEYWORDS=~amd64 ~ppc ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=mirror://gentoo/sim4-20030921.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=d9ac88a2e3ccc00187d880fcca7f5db2 diff --git a/metadata/md5-cache/sci-biology/stride-20011129-r1 b/metadata/md5-cache/sci-biology/stride-20011129-r1 new file mode 100644 index 000000000000..fcecbd16c1a5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/stride-20011129-r1 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Protein secondary structure assignment from atomic coordinates +EAPI=7 +HOMEPAGE=http://webclu.bio.wzw.tum.de/stride/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~ppc ~x86 ~amd64-linux ~x86-linux +LICENSE=STRIDE +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/stride.tar.gz -> stride-20011129.tar.gz https://dev.gentoo.org/~pacho/stride/stride-20060723-update.patch.bz2 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=a98099ba2092ac37edaa2d1816ea88a1 diff --git a/metadata/md5-cache/sci-biology/stride-20060723 b/metadata/md5-cache/sci-biology/stride-20060723 new file mode 100644 index 000000000000..7ec7fec9a697 --- /dev/null +++ b/metadata/md5-cache/sci-biology/stride-20060723 @@ -0,0 +1,12 @@ +DEFINED_PHASES=configure install +DESCRIPTION=Protein secondary structure assignment from atomic coordinates +EAPI=8 +HOMEPAGE=http://webclu.bio.wzw.tum.de/stride/ +INHERIT=toolchain-funcs +KEYWORDS=amd64 ~ppc ~x86 ~amd64-linux ~x86-linux +LICENSE=STRIDE +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=https://webclu.bio.wzw.tum.de/stride/stride.tar.gz -> stride-20030408.tar.gz https://dev.gentoo.org/~pacho/stride/stride-20060723-update-r1.patch.xz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=2616b211128e980f88b295ed6dfc1051 diff --git a/metadata/md5-cache/sci-biology/t-coffee-11.00-r3 b/metadata/md5-cache/sci-biology/t-coffee-11.00-r3 new file mode 100644 index 000000000000..3f33f12c73f5 --- /dev/null +++ b/metadata/md5-cache/sci-biology/t-coffee-11.00-r3 @@ -0,0 +1,12 @@ +DEFINED_PHASES=compile configure install +DESCRIPTION=A multiple sequence alignment package +EAPI=8 +HOMEPAGE=http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html +INHERIT=flag-o-matic toolchain-funcs +KEYWORDS=~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux +LICENSE=GPL-2 +RDEPEND=sci-biology/clustalw sci-chemistry/tm-align +SLOT=0 +SRC_URI=http://www.tcoffee.org/Packages/Beta/Latest/T-COFFEE_distribution_Version_11.00.4466924.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=4f19327a55b73328939540ced2179d21 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..492be4e319a1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 @@ -0,0 +1,16 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=compile configure install prepare +DEPEND=mpi? ( virtual/mpi ) +DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data +EAPI=8 +HOMEPAGE=http://www.tree-puzzle.de +INHERIT=autotools +IUSE=mpi +KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos +LICENSE=GPL-2 +RDEPEND=mpi? ( virtual/mpi ) +RESTRICT=test +SLOT=0 +SRC_URI=http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=5b3f19a3bd68515494075eab507798ef diff --git a/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 new file mode 100644 index 000000000000..854d1ab163c1 --- /dev/null +++ b/metadata/md5-cache/sci-biology/treeviewx-0.5.1-r3 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure prepare +DEPEND=x11-libs/wxGTK:3.0[X] +DESCRIPTION=A phylogenetic tree viewer +EAPI=7 +HOMEPAGE=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ +INHERIT=autotools wxwidgets +KEYWORDS=amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=x11-libs/wxGTK:3.0[X] +SLOT=0 +SRC_URI=http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc wxwidgets 9a707a3f9f1ea7aa703b1e46552291e5 +_md5_=c7a6fb1f3ee6436d674328487c021a24 diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r2 b/metadata/md5-cache/sci-biology/trf-4.04-r2 new file mode 100644 index 000000000000..61f83fd36499 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trf-4.04-r2 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install unpack +DESCRIPTION=Tandem Repeats Finder +EAPI=8 +HOMEPAGE=https://tandem.bu.edu/trf/trf.html +KEYWORDS=amd64 ~x86 +LICENSE=trf +RESTRICT=mirror bindist +SLOT=0 +SRC_URI=https://tandem.bu.edu/trf/downloads/trf404.linux +_md5_=1839ce18db10bbc511a18e93309a3819 diff --git a/metadata/md5-cache/sci-biology/trnascan-se-1.31-r3 b/metadata/md5-cache/sci-biology/trnascan-se-1.31-r3 new file mode 100644 index 000000000000..b3063db80a05 --- /dev/null +++ b/metadata/md5-cache/sci-biology/trnascan-se-1.31-r3 @@ -0,0 +1,13 @@ +BDEPEND=dev-lang/perl:= +DEFINED_PHASES=configure install test +DESCRIPTION=tRNA detection in large-scale genome sequences +EAPI=8 +HOMEPAGE=http://lowelab.ucsc.edu/tRNAscan-SE/ +INHERIT=flag-o-matic perl-functions toolchain-funcs +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +RDEPEND=dev-lang/perl:= +SLOT=0 +SRC_URI=http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> trnascan-se-1.31.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc perl-functions c3fca037246e877693badea0df3b0ef8 +_md5_=52e449bd6a1f0b9bd42d7eaedfc1d9e6 diff --git a/metadata/md5-cache/sci-biology/uchime-4.2.40-r1 b/metadata/md5-cache/sci-biology/uchime-4.2.40-r1 new file mode 100644 index 000000000000..acb62455cbb0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/uchime-4.2.40-r1 @@ -0,0 +1,12 @@ +BDEPEND=>=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 +DEFINED_PHASES=compile configure install prepare test +DESCRIPTION=Fast, accurate chimera detection +EAPI=8 +HOMEPAGE=https://www.drive5.com/usearch/manual/uchime_algo.html +INHERIT=cmake +KEYWORDS=amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +SLOT=0 +SRC_URI=https://www.drive5.com/uchime/uchime4.2.40_src.tar.gz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc multiprocessing 30ead54fa2e2b5f9cd4e612ffc34d0fe ninja-utils 39e7a84b06eff4efd9f2e0c3d1668b98 xdg-utils baea6080dd821f5562d715887954c9d3 cmake fc2f89084f590ac95c004ea95b0d2f80 +_md5_=d6d5b7ba215fd8eaf51d3847f4051df6 diff --git a/metadata/md5-cache/sci-biology/ucsc-genome-browser-260-r1 b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260-r1 new file mode 100644 index 000000000000..d7c68331b2cf --- /dev/null +++ b/metadata/md5-cache/sci-biology/ucsc-genome-browser-260-r1 @@ -0,0 +1,15 @@ +DEFINED_PHASES=compile install postinst prepare prerm setup +DEPEND=dev-libs/openssl:0= media-libs/libpng:0= !<sci-biology/ucsc-genome-browser-223 mysql? ( dev-db/mysql-connector-c:0= ) server? ( virtual/httpd-cgi ) app-arch/unzip app-admin/webapp-config +DESCRIPTION=The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath +EAPI=6 +HOMEPAGE=http://genome.ucsc.edu/ +INHERIT=toolchain-funcs flag-o-matic webapp +IUSE=+mysql +server static-libs vhosts +KEYWORDS=~amd64 ~x86 +LICENSE=blat +RDEPEND=dev-libs/openssl:0= media-libs/libpng:0= !<sci-biology/ucsc-genome-browser-223 mysql? ( dev-db/mysql-connector-c:0= ) server? ( virtual/httpd-cgi ) app-admin/webapp-config +REQUIRED_USE=server? ( mysql ) +SLOT=0 +SRC_URI=http://hgdownload.cse.ucsc.edu/admin/jksrc.v260.zip +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 desktop 021728fdc1b03b36357dbc89489e0f0d edos2unix 33e347e171066657f91f8b0c72ec8773 estack c61c368a76fdf3a82fdf8dbaebea3804 epatch 2b02655f061dfa25067b543539110259 eqawarn c9847c43b3253a276ae2eabddedab3d7 ltprune 97143780d341cc8d8f1d4c6187a36d29 preserve-libs 21162ec96c87041004a75348d97342dd strip-linguas ac3ee41ee2d31d8c41a77c0838320cc7 vcs-clean d271b7bc7e6a009758d7d4ef749174e3 wrapper 4a1902f969e5718126434fc35f3a0d9c eutils d318efeb438bbec051fa5aaf28d0d42c flag-o-matic e5cc383ea8420f92fe3737be790021dc webapp de2d3d345b44597c10d7104a7bcdf7b2 +_md5_=35cb93e40ad2d78c190e860dd3944557 diff --git a/metadata/md5-cache/sci-biology/unafold-3.8-r1 b/metadata/md5-cache/sci-biology/unafold-3.8-r1 new file mode 100644 index 000000000000..c653e8528860 --- /dev/null +++ b/metadata/md5-cache/sci-biology/unafold-3.8-r1 @@ -0,0 +1,14 @@ +BDEPEND=sys-devel/autoconf-archive sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure prepare +DEPEND=media-libs/freeglut media-libs/gd virtual/opengl +DESCRIPTION=Unified Nucleic Acid Folding and hybridization package +EAPI=8 +HOMEPAGE=http://mfold.rna.albany.edu/ +INHERIT=autotools +KEYWORDS=~amd64 ~x86 +LICENSE=unafold +RDEPEND=media-libs/freeglut media-libs/gd virtual/opengl +SLOT=0 +SRC_URI=http://dinamelt.bioinfo.rpi.edu/download/unafold-3.8.tar.bz2 +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde +_md5_=9559cbf8e26b94caa53077c0b5e2c89c diff --git a/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 new file mode 100644 index 000000000000..f8389879cf7b --- /dev/null +++ b/metadata/md5-cache/sci-biology/update-blastdb-12.0.0 @@ -0,0 +1,10 @@ +DEFINED_PHASES=install +DESCRIPTION=update_blastdb.pl for local blast db maintainance +EAPI=7 +HOMEPAGE=http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit +KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +LICENSE=public-domain +RDEPEND=dev-lang/perl !sci-biology/ncbi-tools++ +SLOT=0 +SRC_URI=ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/12_0_0/ncbi_cxx--12_0_0.tar.gz +_md5_=899b0a0aa3b8be8b9530aff68709f438 diff --git a/metadata/md5-cache/sci-biology/vcftools-0.1.16 b/metadata/md5-cache/sci-biology/vcftools-0.1.16 new file mode 100644 index 000000000000..f7812b864983 --- /dev/null +++ b/metadata/md5-cache/sci-biology/vcftools-0.1.16 @@ -0,0 +1,15 @@ +BDEPEND=virtual/pkgconfig sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure prepare +DEPEND=sys-libs/zlib dev-lang/perl:= lapack? 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( virtual/lapack ) +SLOT=0 +SRC_URI=https://github.com/vcftools/vcftools/releases/download/v0.1.16/vcftools-0.1.16.tar.gz +_eclasses_=gnuconfig b6b3e92f8b8c996400074b5f61a59256 toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 libtool 9d3a9a889a6fa62ae794f817c156491b autotools 6ae9a4347149b19a112caa1182d03bde flag-o-matic e5cc383ea8420f92fe3737be790021dc perl-functions c3fca037246e877693badea0df3b0ef8 +_md5_=faeb202e0aded0cb660ea87d6d7be81b diff --git a/metadata/md5-cache/sci-biology/velvet-1.2.10 b/metadata/md5-cache/sci-biology/velvet-1.2.10 new file mode 100644 index 000000000000..5e1972f65bc7 --- /dev/null +++ b/metadata/md5-cache/sci-biology/velvet-1.2.10 @@ -0,0 +1,13 @@ +BDEPEND=doc? ( virtual/latex-base ) +DEFINED_PHASES=compile install prepare test +DESCRIPTION=A sequence assembler for very short reads +EAPI=8 +HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ +INHERIT=flag-o-matic toolchain-funcs +IUSE=doc openmp +KEYWORDS=~amd64 ~x86 +LICENSE=GPL-2 +SLOT=0 +SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 flag-o-matic e5cc383ea8420f92fe3737be790021dc +_md5_=f48eb0348a1ac91d41dde22d3ced2ea1 diff --git a/metadata/md5-cache/sci-biology/wise-2.4.0_alpha-r1 b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha-r1 new file mode 100644 index 000000000000..0dc0ac33637c --- /dev/null +++ b/metadata/md5-cache/sci-biology/wise-2.4.0_alpha-r1 @@ -0,0 +1,15 @@ +BDEPEND=app-shells/tcsh dev-lang/perl virtual/latex-base +DEFINED_PHASES=compile install prepare test +DEPEND=~sci-biology/hmmer-2.3.2 +DESCRIPTION=Intelligent algorithms for DNA searches +EAPI=8 +HOMEPAGE=http://www.ebi.ac.uk/Wise2/ +INHERIT=toolchain-funcs +IUSE=doc +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 https://dev.gentoo.org/~mgorny/dist/wise-2.4.0_alpha-patchset.tar.bz2 +_eclasses_=toolchain-funcs fbbbc99d10168de2926e06da7169b8dc multilib c19072c3cd7ac5cb21de013f7e9832e0 +_md5_=34f9a1f8b8f239e402200b9b5cb4f3cc diff --git a/metadata/md5-cache/sci-biology/yass-1.14-r3 b/metadata/md5-cache/sci-biology/yass-1.14-r3 new file mode 100644 index 000000000000..59c042e2e0d0 --- /dev/null +++ b/metadata/md5-cache/sci-biology/yass-1.14-r3 @@ -0,0 +1,15 @@ +BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71-r5 >=sys-devel/libtool-2.4.7 +DEFINED_PHASES=configure prepare +DEPEND=dmalloc? 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