Biology Project – Gentoo Packages

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Latest Commits

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
- sci-biology/augustus: add 3.5.0
  7fdfd97
  Alfred Wingate authored and Sam James committed on 2025-02-11 01:36:17 UTC
  sci-biology/augustus/augustus-3.5.0.ebuildsci-biology/augustus/Manifest
- sci-biology/augustus: include cstdint for gcc-13
  4639874
  Alfred Wingate authored and Sam James committed on 2025-02-11 01:36:17 UTC
  sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patchsci-biology/augustus/augustus-3.4.0-r3.ebuild
Commits on 2024-12-31
- sci-biology/yass: Remove USE=dmalloc
  d0977ce
  NHOrus authored and Sam James committed on 2024-12-31 14:22:33 UTC
  sci-biology/yass/metadata.xmlsci-biology/yass/yass-1.14-r3.ebuild
Commits on 2024-12-26
- sci-biology/seaview: add binding := to fltk, soname changed
  de9ecbd
  Ionen Wolkens committed on 2024-12-26 17:48:34 UTC
  sci-biology/seaview/seaview-4.6-r2.ebuildsci-biology/seaview/seaview-4.6-r1.ebuild
Commits on 2024-12-24
- sci-libs/dcmtk: add 3.6.9
  1f97cb6
  Sam James committed on 2024-12-24 05:46:21 UTC
  sci-libs/dcmtk/dcmtk-3.6.9.ebuildsci-libs/dcmtk/files/dcmtk-3.6.9-docdir.patchsci-libs/dcmtk/Manifest
Commits on 2024-12-21
- dev-perl/Bio-DB-HTS: Drop old versions
  5e77445
  Matt Turner authored and Sam James committed on 2024-12-21 20:30:56 UTC
  dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0-r1.ebuild
Commits on 2024-12-11
- Move {sys-devel → llvm-core}/clang-runtime
  6aa98b9
  Michał Górny committed on 2024-12-11 11:53:16 UTC
  llvm-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-19.1.4.ebuildllvm-core/clang-runtime/clang-runtime-19.1.5.ebuildllvm-core/clang-runtime/clang-runtime-20.0.0.9999.ebuildllvm-core/clang-runtime/clang-runtime-20.0.0_pre20241207.ebuildllvm-core/clang-runtime/metadata.xmlapp-crypt/libb2/libb2-0.98.1-r3.ebuilddev-libs/oneDNN/oneDNN-3.5.3.ebuilddev-libs/oneDNN/oneDNN-3.6.2.ebuilddev-libs/rocm-comgr/rocm-comgr-5.1.3-r3.ebuilddev-libs/rocm-comgr/rocm-comgr-5.3.3-r2.ebuilddev-libs/rocm-comgr/rocm-comgr-5.4.3-r1.ebuilddev-libs/rocm-comgr/rocm-comgr-5.5.1.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-6.2.4.ebuilddev-util/hip/hip-5.1.3-r4.ebuilddev-util/hip/hip-5.3.3-r3.ebuilddev-util/hip/hip-5.4.3.ebuilddev-util/hip/hip-5.5.1.ebuilddev-util/hip/hip-5.7.1-r2.ebuilddev-util/hip/hip-6.1.1.ebuilddev-util/hip/hip-6.1.2.ebuilddev-util/hip/hip-6.2.4.ebuildgui-wm/wayfire/wayfire-0.9.0.ebuildsys-devel/clang-runtime/clang-runtime-15.0.7.ebuildsys-devel/clang-runtime/clang-runtime-16.0.6.ebuildsys-devel/clang-runtime/clang-runtime-17.0.6.ebuildsys-devel/clang-runtime/clang-runtime-18.1.8.ebuildsys-devel/clang-runtime/clang-runtime-19.1.4.ebuildsys-devel/clang-runtime/clang-runtime-19.1.5.ebuildsys-devel/clang-runtime/clang-runtime-20.0.0.9999.ebuildsys-devel/clang-runtime/clang-runtime-20.0.0_pre20241207.ebuildsys-devel/clang-runtime/metadata.xml...
Commits on 2024-12-06
- dev-libs/igraph: Stabilize 0.10.12 amd64, #945574
  0564775
  Sam James committed on 2024-12-06 07:47:05 UTC
  dev-libs/igraph/igraph-0.10.12.ebuild
Commits on 2024-12-05
- sci-biology/muscle: Stabilize 5.1.0 amd64, #945576
  a0ebc28
  Sam James committed on 2024-12-05 18:30:08 UTC
  sci-biology/muscle/muscle-5.1.0.ebuild
Commits on 2024-12-04
- sci-libs/dcmtk: Stabilize 3.6.8 amd64, #945556
  9c35716
  Sam James committed on 2024-12-04 09:12:32 UTC
  sci-libs/dcmtk/dcmtk-3.6.8.ebuild
Commits on 2024-12-03
- sci-biology/mothur: Stabilize 1.48.0 amd64, #945569
  59a64e3
  Sam James committed on 2024-12-03 11:14:07 UTC
  sci-biology/mothur/mothur-1.48.0.ebuild
- sci-biology/glimmerhmm: Stabilize 3.0.4 amd64, #945559
  165cb77
  Sam James committed on 2024-12-03 11:14:05 UTC
  sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
Commits on 2024-12-01
- dev-libs/igraph: Stabilize 0.10.12 x86, #945574
  21a3e6f
  Jakov Smolić committed on 2024-12-01 22:35:54 UTC
  dev-libs/igraph/igraph-0.10.12.ebuild
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/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