| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: Add python-muon.•••* gnu/packages/bioinformatics.scm (python-muon): New variable.
Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| guix@mawumag.com | 2024-07-01 | 1 | -0/+52 |
| * | gnu: Add python-mofapy2.•••* gnu/packages/bioinformatics.scm (python-mofapy2): New variable.
Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| guix@mawumag.com | 2024-07-01 | 1 | -0/+44 |
| * | gnu: Add r-anpan.•••* gnu/packages/bioinformatics.scm (r-anpan): New variable.
Change-Id: Ia01ba3be7424306674b9c9b2904f1f0cfa66d818
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Afkhami, Navid | 2024-07-01 | 1 | -0/+48 |
| * | gnu: Add r-cmdstanr.•••* gnu/packages/bioinformatics.scm (r-cmdstanr): New variable.
Change-Id: Ic9e83486f7ab7f0e7075343af630c4dcecf597b5
Signed-off-by: Andreas Enge <andreas@enge.fr>
| Afkhami, Navid | 2024-06-30 | 1 | -1/+36 |
| * | gnu: jellyfish: Enable building on all 64bit platforms.•••* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems]: Mark
all 64bit platforms as supported.
Change-Id: Ia79d8052bf6ff347422e4b1ce38dc379d45a9be6
| Efraim Flashner | 2024-06-30 | 1 | -1/+1 |
| * | gnu: Add r-rphyloxml.•••* gnu/packages/bioinformatics.scm (r-rphyloxml): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I5b799986064f2af5fe74454f2e78fea7d9947260
| Afkhami, Navid | 2024-06-28 | 1 | -0/+52 |
| * | gnu: Add r-rnacrosslinkoo.•••* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo): New variable.
Change-Id: I1ca6dcef9c093627c3743d1176e587cf40053ba0
| Afkhami, Navid | 2024-06-28 | 1 | -0/+44 |
| * | gnu: Add r-scent.•••* gnu/packages/bioinformatics.scm (r-scent): New variable.
Change-Id: Ie517c0619683590f630013982e831fad528c1dea
| Afkhami, Navid | 2024-06-18 | 1 | -0/+37 |
| * | gnu: Add python-celltypist.•••* gnu/packages/bioinformatics.scm (python-celltypist): New variable.
Change-Id: I196b7a07955224fe4c641d79729f0facb6367adb
| Ricardo Wurmus | 2024-05-31 | 1 | -0/+47 |
| * | gnu: ensembl-vep: Update to 112.•••* gnu/packages/bioinformatics.scm (ensembl-vep): Update to 112.
[propagated-inputs]: Add perl-list-moreutils.
[native-inputs]: Add perl-test-deep and perl-test-warnings.
Change-Id: I8c7de9f3dbc8c6fe4d1383f9dc215aeba018af0d
| Ricardo Wurmus | 2024-05-22 | 1 | -8/+11 |
| * | gnu: samtools: Fix build on i686-linux.•••* gnu/packages/bioinformatics.scm (samtools)[arguments]: When building
for i686-linux adjust the make-flags to specifically use the sse math
libraries.
Change-Id: I322d521cbe87e10db7c23db8e68bb377db966aa7
| Efraim Flashner | 2024-05-19 | 1 | -0/+5 |
| * | gnu: pigx-rnaseq: Update to 0.1.1.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.1.
Change-Id: I16db332e3559bed5b302f08bd85f31c6c40e9619
| Ricardo Wurmus | 2024-05-15 | 1 | -2/+2 |
| * | gnu: Add r-anndatar.•••* gnu/packages/bioinformatics.scm (r-anndatar): New variable.
Change-Id: I6060c5c15a46c064aa03ec2431a72ea88f925706
| Ricardo Wurmus | 2024-05-13 | 1 | -0/+29 |
| * | gnu: minimap2: Remove included file from gcc.•••* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust custom
'install phase to remove included emmintrin.h header.
Change-Id: Id994dd2bd4a98e8d1c162c4e011fc77b9d5565d2
| Efraim Flashner | 2024-05-12 | 1 | -0/+2 |
| * | gnu: rcas-web: Update to latest commit.•••The latest commit fixes a problem in configure.ac.
* gnu/packages/bioinformatics.scm (rcas-web)[source]: Fetch from git.
[arguments]: Remove 'find-RCAS phase; use G-expression.
[inputs]: Drop labels. Use Guile 3.0.
[native-inputs]: Add autoconf and automake.
Change-Id: I6f1d300df589a99b9493b2857f58d49e468b210e
| Ricardo Wurmus | 2024-05-08 | 1 | -48/+45 |
| * | gnu: r-icellnet: Update to 2.2.1-1.e10ee4a.•••* gnu/packages/bioinformatics.scm (r-icellnet): Update to 2.2.1-1.e10ee4a.
[propagated-inputs]: Add r-complexheatmap and r-circlize.
Change-Id: Ib844f83cb1ca4f88259593153d9e66289307dccc
| Ricardo Wurmus | 2024-05-08 | 1 | -8/+10 |
| * | gnu: bitmapperbs: Limit to x86_64-linux.•••* gnu/packages/bioinformatics.scm (bitmapperbs)[supported-systems]: New
field.
Change-Id: I03484413e5af8e779fe0e5199e456eaab124e8b7
| Efraim Flashner | 2024-05-07 | 1 | -0/+1 |
| * | gnu: minimap2: Fix make-flags.•••* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust the
make-flags to contain actual build flags for all architectures.
Change-Id: I5b4077a25d6d46172ff566ceaa16629ebf066721
| Efraim Flashner | 2024-05-06 | 1 | -3/+1 |
| * | gnu: minimap2: Update to 2.28.•••* gnu/packages/bioinformatics.scm (minimap2): Update to 2.28.
[arguments]: Adjust custom 'install phase to not delete non-existent
file. Remove trailing #t from phase.
Change-Id: Ie6cc21f2b761532f08967efea54d3a12b944f213
| Efraim Flashner | 2024-05-06 | 1 | -6/+3 |
| * | gnu: proteinortho: Add tunable property.•••* gnu/packages/bioinformatics.scm (proteinortho)[properties]: Add
tunable? flag.
Change-Id: If59d5785c8c8e4aedb5b88479da6fba0e9754640
| Efraim Flashner | 2024-05-06 | 1 | -0/+1 |
| * | gnu: proteinortho: Update to 6.3.2.•••* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.3.2.
[source]: Adjust snippet to also delete lapack source tarball.
[arguments]: Rewrite using g-expressions. Add flag to run tests
sequentially. Adjust make-flags for cross-compiling and to set PREFIX.
Delete 'configure and custom 'configure phase. Remove trailing #t from
phases.
Change-Id: I40249e5ac92c26223119b81b4677c08d5ab230e6
| Efraim Flashner | 2024-05-06 | 1 | -33/+28 |
| * | gnu: trust4: Update to 1.1.0.•••* gnu/packages/bioinformatics.scm (trust4): Update to 1.1.0.
Change-Id: I4780038a5db110514e27f07a576166def4063da7
| Ricardo Wurmus | 2024-05-06 | 1 | -2/+2 |
| * | gnu: Add trust4.•••gnu/packages/bioinformatics.scm (trust4): New variable.
Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
| Mădălin Ionel Patrașcu | 2024-05-06 | 1 | -0/+76 |
| * | gnu: Add r-seraster.•••* gnu/packages/bioinformatics.scm (r-seraster): New variable.
Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
| Mădălin Ionel Patrașcu | 2024-05-06 | 1 | -0/+39 |
| * | gnu: Add r-metadeconfoundr.•••* gnu/packages/bioinformatics.scm (r-metadeconfoundr): New variable.
Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
| Mădălin Ionel Patrașcu | 2024-05-06 | 1 | -0/+41 |
| * | gnu: Add python-pyrodigal.•••* gnu/packages/bioinformatics.scm (python-pyrodigal): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
| nafkhamdc | 2024-05-06 | 1 | -0/+41 |
| * | gnu: Add python-pyahocorasick.•••* gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable.
Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| nafkhamdc | 2024-05-06 | 1 | -0/+23 |
| * | gnu: python-liana-py: Update to 1.1.0.•••* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.1.0.
[arguments]: Adjust tests; add phase 'relax-requirements.
[propagated-inputs]: Remove python-mofax; add python-numpy.
[native-inputs]: Remove python-numpy; add python-poetry-core.
Change-Id: I279be08ac3ac73d9a724f59652f2f0d333607696
| Ricardo Wurmus | 2024-05-05 | 1 | -5/+27 |
| * | gnu: python-cooltools: Update to 0.7.0.•••* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
| Ricardo Wurmus | 2024-05-05 | 1 | -11/+3 |
| * | gnu: python-bioframe: Update to 0.6.4.•••* gnu/packages/bioinformatics.scm (python-bioframe): Update to 0.6.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'pre-check phase. Use
#:test-flags to disable tests that require internet access.
[native-inputs]: Add python-hatchling.
[propagated-inputs]: Add python-pyyaml.
Change-Id: Iad1c8c6ef8f52886e398e9c4d2d384c5fce075c6
| Ricardo Wurmus | 2024-05-05 | 1 | -10/+14 |
| * | gnu: python-decoupler-py: Update to 1.6.0.•••* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.
Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
| Ricardo Wurmus | 2024-05-05 | 1 | -64/+55 |
| * | gnu: python-hicexplorer: Update to 3.7.4.•••* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.
Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
| Ricardo Wurmus | 2024-05-05 | 1 | -24/+4 |
| * | gnu: tadbit: Add R to inputs.•••* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal.
Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
| Ricardo Wurmus | 2024-05-05 | 1 | -1/+2 |
| * | gnu: tadbit: Patch for compatibility with latest scipy.•••* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.
Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
| Ricardo Wurmus | 2024-05-05 | 1 | -0/+12 |
| * | gnu: tadbit: Update to 1.0.1-2.2838129.•••* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129.
Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
| Ricardo Wurmus | 2024-05-05 | 1 | -3/+3 |
| * | gnu: python-cooler: Update to 0.9.3.•••* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3.
Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
| Ricardo Wurmus | 2024-05-05 | 1 | -2/+2 |
| * | gnu: python-scikit-bio: Update to 0.6.0.•••* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0.
[source]: Remove patch.
[arguments]: Disable skbio.diversity doctest; remove 'compatibility phase.
[propagated-inputs]: Add python-biom-format; remove python-ipython and
python-matplotlib.
Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed
| Ricardo Wurmus | 2024-05-05 | 1 | -11/+9 |
| * | gnu: python-biom-format: Untangle from python-scikit-bio.•••* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]: Add phase
'pandas-compatibility; disable tests that need sciki-bio.
[propagated-inputs]: Remove python-scikit-bio.
Change-Id: Ifd528d256a1c75962fb05aef5602edbf67a5af26
| Ricardo Wurmus | 2024-05-05 | 1 | -1/+24 |
| * | gnu: tadbit: Use G-expression.•••* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression.
Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
| Ricardo Wurmus | 2024-05-05 | 1 | -23/+22 |
| * | gnu: python-plastid: Replace nose with pytest.•••* gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace
python-nose with python-pytest.
Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
| Ricardo Wurmus | 2024-05-05 | 1 | -1/+1 |
| * | gnu: Add python-metacells.•••* gnu/packages/bioinformatics.scm (python-metacells): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
| Marco Baggio | 2024-05-05 | 1 | -0/+69 |
| * | gnu: Add r-saige.•••* gnu/packages/bioinformatics.scm (r-saige): New variable.
Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
| Ricardo Wurmus | 2024-04-22 | 1 | -0/+56 |
| * | gnu: Add savvy.•••* gnu/packages/bioinformatics.scm (savvy): New variable.
Change-Id: I48dcfad2c6c769778bd79dffa084332da53991ad
| Ricardo Wurmus | 2024-04-22 | 1 | -0/+37 |
| * | gnu: python-deeptools: Replace python-nose with python-pytest.•••* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace
python-nose with python-pytest.
Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
| Ricardo Wurmus | 2024-04-22 | 1 | -1/+1 |
| * | gnu: Add python-cyvcf2.•••* gnu/packages/bioinformatics.scm (python-cyvcf2): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
| Alexis Simon | 2024-04-22 | 1 | -0/+53 |
| * | gnu: java-guava: Update to 31.1.•••* gnu/packages/patches/java-guava-remove-annotation-deps.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/java.scm (java-guava): Update to 31.1.
[source]: Use patch.
(java-guava-futures-failureaccess): New variable.
* gnu/packages/bioinformatics.scm (java-picard, java-picard-2.10.3): Fix for
newer guava.
* gnu/packages/maven.scm (maven): Add java-guava-futures-failureaccess.
Change-Id: Id2553c48e11c6001fb45a0589720cef1551804d9
| Julien Lepiller | 2024-04-20 | 1 | -0/+8 |
| * | gnu: go-github-com-fatih-color: Move to golang-xyz.•••* gnu/packages/golang.scm (go-github-com-fatih-color): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here.
* gnu/packages/bioinformatics.scm: Add (gnu packages golang-xyz) module.
Change-Id: I302327d3426100d7984e6086726396e9fe7f7468
| Sharlatan Hellseher | 2024-04-12 | 1 | -0/+1 |
| * | gnu: python-deeptools: Update to 3.5.5.•••* gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.5.
[build-system]: Replace by pyproject-build-system.
[arguments]: Add phase that fixes 'test/test_tools.py'.
Change-Id: Ibb51939275c96df2c4a1e248a03d683f2f4904ac
Signed-off-by: Christopher Baines <mail@cbaines.net>
| Simon Tournier | 2024-04-09 | 1 | -4/+19 |
| * | gnu: proteinortho: Remove dependency on lapack.•••* gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Romain GARBAGE | 2024-04-04 | 1 | -2/+3 |
| * | gnu: eigensoft: Remove dependency on lapack.•••* gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack.
Change-Id: I9d4adfd64a32333a0d605d4ce1aa998035decf2a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Romain GARBAGE | 2024-04-04 | 1 | -1/+1 |
