Biology Project – Gentoo Packages

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Latest Commits

Commits on 2025-10-05
- sci-biology/uchime: Fix build w/ cmake-4
  f527c12
  Andreas Sturmlechner committed on 2025-10-05 17:44:06 UTC
  sci-biology/uchime/files/CMakeLists.patchsci-biology/uchime/uchime-4.2.40-r1.ebuild
- sci-biology/fasttree: Raise cmake_minimum_required to 3.31
  6001c92
  Andreas Sturmlechner committed on 2025-10-05 17:44:05 UTC
  sci-biology/fasttree/files/CMakeLists.txt
Commits on 2025-09-30
- sci-biology/fasttree: update EAPI 7 -> 8
  916a7e7
  Andreas Sturmlechner committed on 2025-09-30 04:52:22 UTC
  sci-biology/fasttree/fasttree-2.1.11.ebuildsci-biology/fasttree/files/CMakeLists.txt
Commits on 2025-09-02
- */*: destable sparc
  0ad96e8
  Arthur Zamarin committed on 2025-09-02 17:00:14 UTC
  app-accessibility/at-spi2-atk/at-spi2-atk-2.46.0.ebuildapp-accessibility/at-spi2-core/at-spi2-core-2.54.1-r1.ebuildapp-accessibility/espeak-ng/espeak-ng-1.51.ebuildapp-accessibility/espeak-ng/espeak-ng-1.52.0.ebuildapp-accessibility/flite/flite-2.2-r1.ebuildapp-accessibility/flite/flite-2.2-r2.ebuildapp-accessibility/flite/flite-2.2-r3.ebuildapp-accessibility/mbrola-voices/mbrola-voices-0_pre20200331.ebuildapp-accessibility/mbrola/mbrola-3.3-r1.ebuildapp-accessibility/speech-dispatcher/speech-dispatcher-0.11.5.ebuildapp-accessibility/speech-dispatcher/speech-dispatcher-0.12.0-r1.ebuildapp-accessibility/speech-tools/speech-tools-2.5.0-r1.ebuildapp-accessibility/speech-tools/speech-tools-2.5.0-r2.ebuildapp-admin/analog/analog-6.0.17.ebuildapp-admin/apache-tools/apache-tools-2.4.63.ebuildapp-admin/apachetop/apachetop-0.23.2.ebuildapp-admin/augeas/augeas-1.14.1-r1.ebuildapp-admin/awscli/awscli-1.41.14.ebuildapp-admin/conky/conky-1.22.1-r1.ebuildapp-admin/emacs-updater/emacs-updater-1.19.ebuild...
- Move {llvm-core → llvm-runtimes}/clang-runtime
  b8500b6
  Michał Górny committed on 2025-09-02 14:32:22 UTC
  llvm-runtimes/clang-runtime/clang-runtime-15.0.7.ebuildllvm-runtimes/clang-runtime/clang-runtime-16.0.6.ebuildllvm-runtimes/clang-runtime/clang-runtime-17.0.6.ebuildllvm-runtimes/clang-runtime/clang-runtime-18.1.8.ebuildllvm-runtimes/clang-runtime/clang-runtime-19.1.7.ebuildllvm-runtimes/clang-runtime/clang-runtime-20.1.8-r1.ebuildllvm-runtimes/clang-runtime/clang-runtime-20.1.8.ebuildllvm-runtimes/clang-runtime/clang-runtime-21.1.0-r1.ebuildllvm-runtimes/clang-runtime/clang-runtime-21.1.0.ebuildllvm-runtimes/clang-runtime/clang-runtime-22.ebuildllvm-runtimes/clang-runtime/metadata.xmlapp-crypt/libb2/libb2-0.98.1-r3.ebuilddev-libs/rocm-comgr/rocm-comgr-5.7.1.ebuilddev-libs/rocm-comgr/rocm-comgr-6.1.1.ebuilddev-libs/rocm-comgr/rocm-comgr-6.1.2.ebuilddev-libs/rocm-comgr/rocm-comgr-6.3.2-r1.ebuilddev-libs/rocm-comgr/rocm-comgr-6.3.3.ebuilddev-libs/rocm-comgr/rocm-comgr-6.4.1.ebuilddev-libs/rocm-comgr/rocm-comgr-6.4.3.ebuilddev-util/hip/hip-5.7.1-r2.ebuilddev-util/hip/hip-6.1.1.ebuilddev-util/hip/hip-6.1.2.ebuildgui-wm/wayfire/wayfire-0.10.0.ebuildgui-wm/wayfire/wayfire-0.9.0-r1.ebuildgui-wm/wayfire/wayfire-9999.ebuildllvm-core/clang-common/clang-common-15.0.7-r10.ebuildllvm-core/clang-common/clang-common-16.0.6-r6.ebuildllvm-core/clang-common/clang-common-17.0.6-r10.ebuildllvm-core/clang-common/clang-common-17.0.6-r9.ebuildllvm-core/clang-common/clang-common-18.1.8-r3.ebuildllvm-core/clang-common/clang-common-19.1.7.ebuildllvm-core/clang-runtime/clang-runtime-15.0.7.ebuildllvm-core/clang-runtime/clang-runtime-16.0.6.ebuildllvm-core/clang-runtime/clang-runtime-17.0.6.ebuildllvm-core/clang-runtime/clang-runtime-18.1.8.ebuildllvm-core/clang-runtime/clang-runtime-19.1.7.ebuildllvm-core/clang-runtime/clang-runtime-20.1.8-r1.ebuildllvm-core/clang-runtime/clang-runtime-20.1.8.ebuildllvm-core/clang-runtime/clang-runtime-21.1.0-r1.ebuildllvm-core/clang-runtime/clang-runtime-21.1.0.ebuildllvm-core/clang-runtime/clang-runtime-22.ebuildllvm-core/clang-runtime/metadata.xml...
Commits on 2025-08-05
- sci-biology/hmmer: use dot-a.eclass
  a738cfe
  Eli Schwartz committed on 2025-08-05 19:53:32 UTC
  sci-biology/hmmer/hmmer-2.3.2-r6.ebuildsci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
Commits on 2025-08-02
- sci-biology/pysam: add 0.23.3
  18dd27b
  Nowa Ammerlaan committed on 2025-08-02 11:29:31 UTC
  sci-biology/pysam/pysam-0.23.3.ebuildsci-biology/pysam/Manifestsci-biology/pysam/pysam-9999.ebuild
Commits on 2025-07-29
- sci-biology/clustal-omega: use dot-a.eclass
  d28f6ef
  Eli Schwartz committed on 2025-07-29 03:34:24 UTC
  sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild
Commits on 2025-07-05
- sci-biology/unafold: add missing Perl BDEPENDs
  74dd2b2
  Sam James committed on 2025-07-05 05:09:28 UTC
  sci-biology/unafold/unafold-3.8-r1.ebuild
Commits on 2025-06-22
- sci-biology/bcftools: add 1.22
  a05f470
  David Seifert committed on 2025-06-22 15:33:13 UTC
  sci-biology/bcftools/bcftools-1.22.ebuildsci-biology/bcftools/Manifest
- sci-biology/samtools: add 1.22
  a35ac16
  David Seifert committed on 2025-06-22 15:33:11 UTC
  sci-biology/samtools/samtools-1.22.ebuildsci-biology/samtools/Manifest
- sci-libs/htslib: add 1.22
  2d54b4f
  David Seifert committed on 2025-06-22 15:33:09 UTC
  sci-libs/htslib/htslib-1.22.ebuildsci-libs/htslib/Manifest
Commits on 2025-06-09
- sci-libs/dcmtk: add dev-libs/libxml2 subslot op for incoming ABI break
  0582a42
  Alfred Wingate authored and Sam James committed on 2025-06-09 03:11:22 UTC
  sci-libs/dcmtk/dcmtk-3.6.7-r2.ebuildsci-libs/dcmtk/dcmtk-3.6.8-r1.ebuildsci-libs/dcmtk/dcmtk-3.6.9-r1.ebuildsci-libs/dcmtk/dcmtk-3.6.7-r1.ebuildsci-libs/dcmtk/dcmtk-3.6.8.ebuildsci-libs/dcmtk/dcmtk-3.6.9.ebuild
- sci-biology/newick-utils: add dev-libs/libxml2 subslot op for incoming ABI break
  08ee8c9
  Alfred Wingate authored and Sam James committed on 2025-06-09 03:11:17 UTC
  sci-biology/newick-utils/newick-utils-1.6-r3.ebuildsci-biology/newick-utils/newick-utils-1.6-r2.ebuild
- dev-libs/igraph: add dev-libs/libxml2 subslot op for incoming ABI break
  a7bbb8d
  Alfred Wingate authored and Sam James committed on 2025-06-09 03:09:50 UTC
  dev-libs/igraph/igraph-0.10.11-r1.ebuilddev-libs/igraph/igraph-0.10.12-r1.ebuilddev-libs/igraph/igraph-0.10.15-r1.ebuilddev-libs/igraph/igraph-0.10.11.ebuilddev-libs/igraph/igraph-0.10.12.ebuilddev-libs/igraph/igraph-0.10.15.ebuild
Commits on 2025-05-27
- sci-biology/biopython: remove unused patch(es)
  baa9423
  Michael Mair-Keimberger authored and Sam James committed on 2025-05-27 08:27:36 UTC
  sci-biology/biopython/files/biopython-1.81-python3.12.patchsci-biology/biopython/files/biopython-1.81-reportlab4.patch
Commits on 2025-05-22
- sci-biology/fasttree: add github upstream metadata
  788ba76
  Sam James committed on 2025-05-22 01:02:12 UTC
  sci-biology/fasttree/metadata.xml
Commits on 2025-05-21
- sci-biology/bamtools: drop 2.5.2, 2.5.2-r1
  fb8d7bd
  Andreas Sturmlechner committed on 2025-05-21 19:20:54 UTC
  sci-biology/bamtools/Manifestsci-biology/bamtools/bamtools-2.5.2-r1.ebuildsci-biology/bamtools/bamtools-2.5.2.ebuildsci-biology/bamtools/files/bamtools-2.5.2-cmake.patch
- sci-biology/bamtools: Stabilize 2.5.3 amd64, #956330
  5cb0d7a
  Arthur Zamarin committed on 2025-05-21 10:56:43 UTC
  sci-biology/bamtools/bamtools-2.5.3.ebuild
Commits on 2025-05-20
- sci-biology/augustus: drop 2.5.5
  2c86280
  Andreas Sturmlechner committed on 2025-05-20 19:12:22 UTC
  sci-biology/augustus/Manifestsci-biology/augustus/augustus-2.5.5.ebuildsci-biology/augustus/files/augustus-2.5.5-sane-build.patch
Commits on 2025-05-18
- sci-biology/bamtools: add 2.5.3
  aa34c5e
  David Seifert committed on 2025-05-18 08:27:44 UTC
  sci-biology/bamtools/bamtools-2.5.3.ebuildsci-biology/bamtools/Manifest
Commits on 2025-05-17
- sci-biology/treeviewx: slot op on x11-libs/wxGTK
  f5acafd
  David Seifert committed on 2025-05-17 14:57:29 UTC
  sci-biology/treeviewx/treeviewx-0.5.1.20100823_p4-r1.ebuildsci-biology/treeviewx/treeviewx-0.5.1.20100823_p4.ebuild
Commits on 2025-05-16
- dev-python/intervaltree: enable py3.14
  0b14dc2
  Arthur Zamarin committed on 2025-05-16 20:07:45 UTC
  dev-python/intervaltree/intervaltree-3.1.0-r1.ebuild
Commits on 2025-05-01
- sci-biology/bowtie: Remove old
  dc22375
  Michał Górny committed on 2025-05-01 11:36:04 UTC
  sci-biology/bowtie/Manifestsci-biology/bowtie/bowtie-2.4.4.ebuild
Commits on 2025-04-29
- sci-biology/bedtools: drop 2.30.0
  2f6e857
  Alfred Wingate authored and Sam James committed on 2025-04-29 19:37:58 UTC
  sci-biology/bedtools/Manifestsci-biology/bedtools/bedtools-2.30.0.ebuildsci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patchsci-biology/bedtools/files/bedtools-2.29.2-python.patchsci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch
- sci-biology/bedtools: enable py3.13
  0532f40
  Alfred Wingate authored and Sam James committed on 2025-04-29 19:37:58 UTC
  sci-biology/bedtools/bedtools-2.31.1.ebuild
Commits on 2025-04-24
- sci-biology/bamtools: update EAPI 7 -> 8 for live ebuild
  cf86189
  NHOrus authored and Sam James committed on 2025-04-24 19:11:35 UTC
  sci-biology/bamtools/bamtools-9999.ebuild
- sci-biology/bamtools: update EAPI 7 -> 8, fix build with CMake 4
  069e8bd
  NHOrus authored and Sam James committed on 2025-04-24 19:11:34 UTC
  sci-biology/bamtools/bamtools-2.5.2-r1.ebuildsci-biology/bamtools/files/bamtools-2.5.2-cmake.patch
Commits on 2025-04-18
- dev-libs/igraph: add 0.10.15
  fe01185
  David Seifert committed on 2025-04-18 17:19:08 UTC
  dev-libs/igraph/igraph-0.10.15.ebuilddev-libs/igraph/Manifest
Commits on 2025-04-17
- sci-biology/fasta: implicit declaration of function ftello
  fc53999
  Brahmajit Das authored and Nowa Ammerlaan committed on 2025-04-17 10:02:23 UTC
  sci-biology/fasta/fasta-36.3.8i-r1.ebuildsci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch
Commits on 2025-04-14
- sci-libs/htslib: Stabilize 1.20 amd64, #920140
  e023423
  Sam James committed on 2025-04-14 15:57:57 UTC
  sci-libs/htslib/htslib-1.20.ebuild
- sci-biology/samtools: Stabilize 1.20 amd64, #920140
  01264aa
  Sam James committed on 2025-04-14 15:57:56 UTC
  sci-biology/samtools/samtools-1.20.ebuild
- sci-biology/bamtools: Stabilize 2.5.2 amd64, #920140
  4d9daad
  Sam James committed on 2025-04-14 15:57:55 UTC
  sci-biology/bamtools/bamtools-2.5.2.ebuild
- sci-biology/augustus: Stabilize 3.4.0-r3 amd64, #920140
  62bb07c
  Sam James committed on 2025-04-14 15:57:55 UTC
  sci-biology/augustus/augustus-3.4.0-r3.ebuild
Commits on 2025-04-09
- sci-biology/bfast: drop 0.7.0a
  19ec106
  Arthur Zamarin committed on 2025-04-09 17:31:40 UTC
  sci-biology/bfast/bfast-0.7.0a.ebuild
Commits on 2025-04-07
- sci-biology/bfast: update EAPI 7 -> 8, fix build with C99
  50d9851
  NHOrus authored and Arthur Zamarin committed on 2025-04-07 18:59:20 UTC
  sci-biology/bfast/bfast-0.7.0a-r1.ebuildsci-biology/bfast/files/bfast-0.7.0a-gzeof.patch
Commits on 2025-04-03
- sci-biology/biopython: add 1.85, drop 1.81-r1
  1052e61
  Alexey Shvetsov committed on 2025-04-03 18:02:14 UTC
  sci-biology/biopython/biopython-1.85.ebuildsci-biology/biopython/Manifestsci-biology/biopython/biopython-1.81-r1.ebuild
Commits on 2025-03-25
- sci-biology/bwa: note that filter-lto has been fixed upstream
  771184d
  Eli Schwartz committed on 2025-03-25 04:11:07 UTC
  sci-biology/bwa/bwa-0.7.17.ebuild
- sci-biology/bwa: add bug link to patches...
  0957b47
  Eli Schwartz committed on 2025-03-25 04:11:07 UTC
  sci-biology/bwa/files/bwa-0.7.17-Makefile.patchsci-biology/bwa/files/bwa-0.7.17-gcc-10.patch
Commits on 2025-03-22
- sci-biology/pysam: Remove old
  f1a1cfe
  Michał Górny committed on 2025-03-22 20:06:33 UTC
  sci-biology/pysam/Manifestsci-biology/pysam/pysam-0.22.1.ebuild
Commits on 2025-03-21
- sci-biology/pysam: sync live build
  485c37a
  Quincy Fleming authored and Nowa Ammerlaan committed on 2025-03-21 14:59:02 UTC
  sci-biology/pysam/pysam-9999.ebuild
- sci-biology/pysam: add 0.23.0
  216304d
  Quincy Fleming authored and Nowa Ammerlaan committed on 2025-03-21 14:59:01 UTC
  sci-biology/pysam/pysam-0.23.0.ebuildsci-biology/pysam/Manifest
- sci-biology/samtools: add 1.21
  17e86ad
  Quincy Fleming authored and Nowa Ammerlaan committed on 2025-03-21 14:59:00 UTC
  sci-biology/samtools/samtools-1.21.ebuildsci-biology/samtools/Manifest
- sci-biology/bcftools: add 1.21
  76e614a
  Quincy Fleming authored and Nowa Ammerlaan committed on 2025-03-21 14:58:59 UTC
  sci-biology/bcftools/bcftools-1.21.ebuildsci-biology/bcftools/Manifest
- sci-libs/htslib: add 1.21
  5113338
  Quincy Fleming authored and Nowa Ammerlaan committed on 2025-03-21 14:58:58 UTC
  sci-libs/htslib/htslib-1.21.ebuildsci-libs/htslib/Manifest
Commits on 2025-03-10
- sci-libs/dcmtk: Stabilize 3.6.9 amd64, #951088
  20e6de2
  Sam James committed on 2025-03-10 22:42:37 UTC
  sci-libs/dcmtk/dcmtk-3.6.9.ebuild
Commits on 2025-02-27
- dev-python/intervaltree: Enable pypy3.11
  bcf18e4
  Michał Górny committed on 2025-02-27 20:57:16 UTC
  dev-python/intervaltree/intervaltree-3.1.0-r1.ebuild
Commits on 2025-02-24
- sci-biology/yass: Fix build with USE=lowmem
  f2e3846
  NHOrus authored and Sam James committed on 2025-02-24 21:25:54 UTC
  sci-biology/yass/files/yass-1.14-lowmem-define.patchsci-biology/yass/yass-1.14-r4.ebuildsci-biology/yass/yass-1.14-r3.ebuild
Commits on 2025-02-13
- sci-biology/augustus: fix gcc15 build
  eb66870
  Alfred Wingate authored and Sam James committed on 2025-02-13 08:45:32 UTC
  sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patchsci-biology/augustus/augustus-3.5.0.ebuild
Commits on 2025-02-11
- sci-biology/augustus: fix phase definition order
  b9a680c
  Sam James committed on 2025-02-11 01:37:12 UTC
  sci-biology/augustus/augustus-3.5.0.ebuild