Biology Project – Gentoo Packages

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Latest Commits

Commits on 2024-09-23
- sci-biology/sim4: fix pkgcheck issues
  c57e8e6
  Filip Kobierski authored and Andrew Ammerlaan committed on 2024-09-23 14:51:02 UTC
  sci-biology/sim4/sim4-20030921-r2.ebuild
- sci-biology/clustalx: remove empty IUSE
  debd83c
  Filip Kobierski authored and Andrew Ammerlaan committed on 2024-09-23 14:51:01 UTC
  sci-biology/clustalx/clustalx-2.1-r3.ebuild
- sci-biology/embassy-phylipnew: mark as LTO-unsafe
  c094eb7
  Eli Schwartz committed on 2024-09-23 00:15:49 UTC
  sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
- sci-biology/embassy-mse: mark as LTO-unsafe
  2eef92f
  Eli Schwartz committed on 2024-09-23 00:15:49 UTC
  sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
- sci-biology/embassy-esim4: mark as LTO-unsafe
  5d1f2bf
  Eli Schwartz committed on 2024-09-23 00:15:49 UTC
  sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
Commits on 2024-09-01
- sci-biology/amap: drop 2.2-r5
  b99f087
  Volkmar W. Pogatzki authored and Miroslav Šulc committed on 2024-09-01 09:56:20 UTC
  sci-biology/amap/amap-2.2-r5.ebuild
Commits on 2024-08-27
- sci-biology/amap: build with java-pkg-simple, add apidocs
  810687b
  Volkmar W. Pogatzki authored and Miroslav Šulc committed on 2024-08-27 07:40:04 UTC
  sci-biology/amap/amap-2.2-r6.ebuild
Commits on 2024-08-22
- sci-biology/fasta: add 36.3.8i
  17f6c86
  Eli Schwartz committed on 2024-08-22 04:17:11 UTC
  sci-biology/fasta/fasta-36.3.8i.ebuildsci-biology/fasta/Manifest
- sci-biology/fasta: mark as LTO-unsafe
  d9f0a90
  Eli Schwartz committed on 2024-08-22 04:17:11 UTC
  sci-biology/fasta/fasta-36.3.8h-r1.ebuild
- sci-biology/fasta: remove tcsh as a test dependency, drop IUSE
  e13c18b
  Eli Schwartz committed on 2024-08-22 04:17:11 UTC
  sci-biology/fasta/fasta-36.3.8h-r1.ebuild
Commits on 2024-07-30
- sci-biology/bowtie: enable py3.12
  9de8c67
  Pacho Ramos committed on 2024-07-30 21:11:51 UTC
  sci-biology/bowtie/bowtie-2.5.1.ebuild
Commits on 2024-07-05
- sci-biology/treeviewx: drop 0.5.1-r3
  9417931
  Pacho Ramos committed on 2024-07-05 17:48:55 UTC
  sci-biology/treeviewx/Manifestsci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patchsci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patchsci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patchsci-biology/treeviewx/files/treeviewx-0.5.1-svg.patchsci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patchsci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patchsci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patchsci-biology/treeviewx/files/treeviewx-wxt.patchsci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild
Commits on 2024-06-23
- dev-libs/igraph: drop 0.10.4-r1, 0.10.10
  522f8c2
  David Seifert committed on 2024-06-23 20:49:09 UTC
  dev-libs/igraph/Manifestdev-libs/igraph/files/808c083fbe661207ee8f0fcd3be5096b5dc17d0d.patchdev-libs/igraph/igraph-0.10.10.ebuilddev-libs/igraph/igraph-0.10.4-r1.ebuild
Commits on 2024-06-05
- sci-biology/biopython: enable py3.12
  bf920df
  Alexey Shvetsov committed on 2024-06-05 17:22:07 UTC
  sci-biology/biopython/biopython-1.81-r1.ebuild
Commits on 2024-06-01
- sci-biology/ucsc-genome-browser: BDEPEND on cpio
  443760b
  Sam James committed on 2024-06-01 23:20:12 UTC
  sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
- sci-biology/ucsc-genome-browser: EAPI 8
  7955b03
  Sam James committed on 2024-06-01 23:19:09 UTC
  sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuildsci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
- sci-biology/ucsc-genome-browser: fix USE=-server
  cdb7db9
  Sam James committed on 2024-06-01 23:15:44 UTC
  sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
- sci-biology/ucsc-genome-browser: workaround modern C issues
  b7cf0f3
  Sam James committed on 2024-06-01 23:15:05 UTC
  sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
Commits on 2024-05-24
- sci-biology/pysam: drop 0.21.0
  a300fad
  David Seifert committed on 2024-05-24 09:54:01 UTC
  sci-biology/pysam/Manifestsci-biology/pysam/files/pysam-0.21.0-cython-3.patchsci-biology/pysam/pysam-0.21.0.ebuild
- sci-biology/pysam: add 0.22.1
  baa6726
  David Seifert committed on 2024-05-24 09:53:59 UTC
  sci-biology/pysam/pysam-0.22.1.ebuildsci-biology/pysam/Manifest
- sci-biology/bcftools: add 1.20
  4cb7398
  David Seifert committed on 2024-05-24 08:59:51 UTC
  sci-biology/bcftools/bcftools-1.20.ebuildsci-biology/bcftools/Manifest
- sci-biology/samtools: add 1.20
  6da5b35
  David Seifert committed on 2024-05-24 08:59:50 UTC
  sci-biology/samtools/samtools-1.20.ebuildsci-biology/samtools/Manifest
- sci-libs/htslib: add 1.20
  dda90e9
  David Seifert committed on 2024-05-24 08:59:49 UTC
  sci-libs/htslib/htslib-1.20.ebuildsci-libs/htslib/Manifest
- sci-libs/htslib: drop 1.17
  5fd841a
  David Seifert committed on 2024-05-24 08:59:48 UTC
  sci-libs/htslib/Manifestsci-libs/htslib/htslib-1.17.ebuild
- sci-biology/samtools: drop 1.17
  3e20bda
  David Seifert committed on 2024-05-24 08:59:46 UTC
  sci-biology/samtools/Manifestsci-biology/samtools/samtools-1.17.ebuild
- sci-biology/bcftools: drop 1.17
  1af6966
  David Seifert committed on 2024-05-24 08:59:45 UTC
  sci-biology/bcftools/Manifestsci-biology/bcftools/bcftools-1.17.ebuild
- sci-biology/raxml: drop 7.2.6
  ccce71a
  David Seifert committed on 2024-05-24 08:44:40 UTC
  sci-biology/raxml/Manifestsci-biology/raxml/files/raxml-7.2.6-makefile.patchsci-biology/raxml/raxml-7.2.6.ebuild
- sci-biology/raxml: add 8.2.13
  48c3969
  David Seifert committed on 2024-05-24 08:44:39 UTC
  sci-biology/raxml/files/raxml-8.2.13-makefile.patchsci-biology/raxml/raxml-8.2.13.ebuildsci-biology/raxml/Manifestsci-biology/raxml/metadata.xml
Commits on 2024-05-22
- dev-perl/Bio-DB-HTS: EAPI 8, rely on eclass impls
  046b0c6
  Sam James committed on 2024-05-22 02:17:53 UTC
  dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0-r2.ebuild
Commits on 2024-05-17
- dev-python/intervaltree: Enable py3.13
  784d26d
  Michał Górny committed on 2024-05-17 18:40:42 UTC
  dev-python/intervaltree/intervaltree-3.1.0-r1.ebuild
Commits on 2024-05-09
- dev-libs/igraph: Stabilize 0.10.11 amd64, #931649
  ad3c513
  Sam James committed on 2024-05-09 21:45:52 UTC
  dev-libs/igraph/igraph-0.10.11.ebuild
- dev-libs/igraph: Stabilize 0.10.11 x86, #931649
  a1a87fc
  Sam James committed on 2024-05-09 21:45:51 UTC
  dev-libs/igraph/igraph-0.10.11.ebuild
- dev-libs/igraph: add 0.10.12
  6de601b
  Sam James committed on 2024-05-09 20:42:35 UTC
  dev-libs/igraph/igraph-0.10.12.ebuilddev-libs/igraph/Manifest
- dev-libs/igraph: update LICENSE
  f699a76
  Sam James committed on 2024-05-09 20:38:21 UTC
  dev-libs/igraph/igraph-0.10.10.ebuilddev-libs/igraph/igraph-0.10.11.ebuilddev-libs/igraph/igraph-0.10.4-r1.ebuild
- dev-libs/igraph: disable -Werror
  c5e3d8c
  Sam James committed on 2024-05-09 20:37:45 UTC
  dev-libs/igraph/igraph-0.10.10.ebuilddev-libs/igraph/igraph-0.10.11.ebuilddev-libs/igraph/igraph-0.10.4-r1.ebuild
- sci-biology/hmmer: Add missing include into configure
  4919e10
  NHOrus authored and Sam James committed on 2024-05-09 01:09:05 UTC
  sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patchsci-biology/hmmer/hmmer-2.3.2-r6.ebuildsci-biology/hmmer/hmmer-2.3.2-r5.ebuild
Commits on 2024-05-08
- sci-biology/paml: restore ~x86
  c80ef33
  Sam James committed on 2024-05-08 16:56:06 UTC
  sci-biology/paml/paml-4.10.7.ebuild
- sci-biology/paml: respect CC, CPPFLAGS, LDFLAGS
  26ed15e
  Sam James committed on 2024-05-08 16:56:05 UTC
  sci-biology/paml/files/paml-4.10.7-LDFLAGS.patchsci-biology/paml/paml-4.10.7.ebuild
- sci-biology/paml: add 4.10.7
  8a73a8d
  NHOrus authored and Sam James committed on 2024-05-08 16:56:04 UTC
  sci-biology/paml/paml-4.10.7.ebuildsci-biology/paml/Manifestsci-biology/paml/metadata.xml
- sci-biology/velvet: fixup whitespace & openmp check
  db6cf7a
  Sam James committed on 2024-05-08 10:45:15 UTC
  sci-biology/velvet/velvet-1.2.10.ebuild
- sci-biology/velvet: scrub patch, add bug ref
  d33156b
  Sam James committed on 2024-05-08 10:44:00 UTC
  sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch
- sci-biology/velvet: Fix incompatible pointer types in 1.2.10
  d11fa81
  NHOrus authored and Sam James committed on 2024-05-08 10:43:28 UTC
  sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patchsci-biology/velvet/velvet-1.2.10.ebuild
Commits on 2024-04-30