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* gnu: Add r-scent.Afkhami, Navid2024-06-18
| | | | | | * gnu/packages/bioinformatics.scm (r-scent): New variable. Change-Id: Ie517c0619683590f630013982e831fad528c1dea
* gnu: Add python-celltypist.Ricardo Wurmus2024-05-31
| | | | | | * gnu/packages/bioinformatics.scm (python-celltypist): New variable. Change-Id: I196b7a07955224fe4c641d79729f0facb6367adb
* gnu: ensembl-vep: Update to 112.Ricardo Wurmus2024-05-22
| | | | | | | | * 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
* gnu: samtools: Fix build on i686-linux.Efraim Flashner2024-05-19
| | | | | | | | * 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
* gnu: pigx-rnaseq: Update to 0.1.1.Ricardo Wurmus2024-05-15
| | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.1. Change-Id: I16db332e3559bed5b302f08bd85f31c6c40e9619
* gnu: Add r-anndatar.Ricardo Wurmus2024-05-13
| | | | | | * gnu/packages/bioinformatics.scm (r-anndatar): New variable. Change-Id: I6060c5c15a46c064aa03ec2431a72ea88f925706
* gnu: minimap2: Remove included file from gcc.Efraim Flashner2024-05-12
| | | | | | | * gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust custom 'install phase to remove included emmintrin.h header. Change-Id: Id994dd2bd4a98e8d1c162c4e011fc77b9d5565d2
* gnu: rcas-web: Update to latest commit.Ricardo Wurmus2024-05-08
| | | | | | | | | | | 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
* gnu: r-icellnet: Update to 2.2.1-1.e10ee4a.Ricardo Wurmus2024-05-08
| | | | | | | * gnu/packages/bioinformatics.scm (r-icellnet): Update to 2.2.1-1.e10ee4a. [propagated-inputs]: Add r-complexheatmap and r-circlize. Change-Id: Ib844f83cb1ca4f88259593153d9e66289307dccc
* gnu: bitmapperbs: Limit to x86_64-linux.Efraim Flashner2024-05-07
| | | | | | | * gnu/packages/bioinformatics.scm (bitmapperbs)[supported-systems]: New field. Change-Id: I03484413e5af8e779fe0e5199e456eaab124e8b7
* gnu: minimap2: Fix make-flags.Efraim Flashner2024-05-06
| | | | | | | * gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust the make-flags to contain actual build flags for all architectures. Change-Id: I5b4077a25d6d46172ff566ceaa16629ebf066721
* gnu: minimap2: Update to 2.28.Efraim Flashner2024-05-06
| | | | | | | | * 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
* gnu: proteinortho: Add tunable property.Efraim Flashner2024-05-06
| | | | | | | * gnu/packages/bioinformatics.scm (proteinortho)[properties]: Add tunable? flag. Change-Id: If59d5785c8c8e4aedb5b88479da6fba0e9754640
* gnu: proteinortho: Update to 6.3.2.Efraim Flashner2024-05-06
| | | | | | | | | | | * 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
* gnu: trust4: Update to 1.1.0.Ricardo Wurmus2024-05-06
| | | | | | * gnu/packages/bioinformatics.scm (trust4): Update to 1.1.0. Change-Id: I4780038a5db110514e27f07a576166def4063da7
* gnu: Add trust4.Mădălin Ionel Patrașcu2024-05-06
| | | | | | gnu/packages/bioinformatics.scm (trust4): New variable. Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
* gnu: Add r-seraster.Mădălin Ionel Patrașcu2024-05-06
| | | | | | * gnu/packages/bioinformatics.scm (r-seraster): New variable. Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
* gnu: Add r-metadeconfoundr.Mădălin Ionel Patrașcu2024-05-06
| | | | | | * gnu/packages/bioinformatics.scm (r-metadeconfoundr): New variable. Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
* gnu: Add python-pyrodigal.nafkhamdc2024-05-06
| | | | | | | | * gnu/packages/bioinformatics.scm (python-pyrodigal): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
* gnu: Add python-pyahocorasick.nafkhamdc2024-05-06
| | | | | | | * gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable. Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python-liana-py: Update to 1.1.0.Ricardo Wurmus2024-05-05
| | | | | | | | | * 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
* gnu: python-cooltools: Update to 0.7.0.Ricardo Wurmus2024-05-05
| | | | | | | | * gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
* gnu: python-bioframe: Update to 0.6.4.Ricardo Wurmus2024-05-05
| | | | | | | | | | | * 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
* gnu: python-decoupler-py: Update to 1.6.0.Ricardo Wurmus2024-05-05
| | | | | | | * gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0. [arguments]: Do not disable test_plot_volcano test. Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
* gnu: python-hicexplorer: Update to 3.7.4.Ricardo Wurmus2024-05-05
| | | | | | | | | * 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
* gnu: tadbit: Add R to inputs.Ricardo Wurmus2024-05-05
| | | | | | * gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal. Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
* gnu: tadbit: Patch for compatibility with latest scipy.Ricardo Wurmus2024-05-05
| | | | | | | * gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase 'scipy-compatibility. Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
* gnu: tadbit: Update to 1.0.1-2.2838129.Ricardo Wurmus2024-05-05
| | | | | | * gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129. Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
* gnu: python-cooler: Update to 0.9.3.Ricardo Wurmus2024-05-05
| | | | | | * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3. Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
* gnu: python-scikit-bio: Update to 0.6.0.Ricardo Wurmus2024-05-05
| | | | | | | | | | | | * 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
* gnu: python-biom-format: Untangle from python-scikit-bio.Ricardo Wurmus2024-05-05
| | | | | | | | * 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
* gnu: tadbit: Use G-expression.Ricardo Wurmus2024-05-05
| | | | | | * gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression. Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
* gnu: python-plastid: Replace nose with pytest.Ricardo Wurmus2024-05-05
| | | | | | | * gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
* gnu: Add python-metacells.Marco Baggio2024-05-05
| | | | | | | * gnu/packages/bioinformatics.scm (python-metacells): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
* gnu: Add r-saige.Ricardo Wurmus2024-04-22
| | | | | | * gnu/packages/bioinformatics.scm (r-saige): New variable. Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
* gnu: Add savvy.Ricardo Wurmus2024-04-22
| | | | | | * gnu/packages/bioinformatics.scm (savvy): New variable. Change-Id: I48dcfad2c6c769778bd79dffa084332da53991ad
* gnu: python-deeptools: Replace python-nose with python-pytest.Ricardo Wurmus2024-04-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
* gnu: Add python-cyvcf2.Alexis Simon2024-04-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-cyvcf2): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
* gnu: java-guava: Update to 31.1.Julien Lepiller2024-04-20
| | | | | | | | | | | | | | * 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
* gnu: go-github-com-fatih-color: Move to golang-xyz.Sharlatan Hellseher2024-04-12
| | | | | | | | | * 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
* gnu: python-deeptools: Update to 3.5.5.Simon Tournier2024-04-09
| | | | | | | | | * 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>
* gnu: proteinortho: Remove dependency on lapack.Romain GARBAGE2024-04-04
| | | | | | * gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: eigensoft: Remove dependency on lapack.Romain GARBAGE2024-04-04
| | | | | | | * gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack. Change-Id: I9d4adfd64a32333a0d605d4ce1aa998035decf2a Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: plink-ng: Remove lapack dep.Romain GARBAGE2024-04-04
| | | | | | | * gnu/packages/bioinformatics.scm (plink-ng): Remove dependency to lapack. Change-Id: I4d14789c42dc216244872d70120efeeb97127a62 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: plink: Switch to openblas.Romain GARBAGE2024-04-04
| | | | | | | | * gnu/packages/bioinformatics.scm (plink): Switch input dependency from lapack to openblas. Change-Id: I8066a50c880b72a77ba00c2bc39403e212605b9d Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-pairadise.Ricardo Wurmus2024-03-21
| | | | | | * gnu/packages/bioinformatics.scm (r-pairadise): New variable. Change-Id: I7314d43c75ed008942757feb878628d1ac855f31
* gnu: Add pairadise.Ricardo Wurmus2024-03-21
| | | | | | * gnu/packages/bioinformatics.scm (pairadise): New variable. Change-Id: I4ad543dea3ddcafd5cbf07623f1faaabb954ba40
* gnu: r-dyngen: Move to (gnu packages cran).Ricardo Wurmus2024-03-19
| | | | | | | * gnu/packages/bioinformatics.scm (r-dyngen): Move variable from here... * gnu/packages/cran.scm (r-dyngen): ...to here. Change-Id: Id181200fb4cbf268542d93e79e43fdeffa99410d
* gnu: r-tictoc: Update to 1.2.1.Ricardo Wurmus2024-03-19
| | | | | | | * gnu/packages/bioinformatics.scm (r-tictoc): Move variable from here... * gnu/packages/cran.scm (r-tictoc): ...to here; update to 1.2.1. Change-Id: I3fc9dde3928a6c5cbe0e25eba8ec001c16e2b66f
* gnu: Add morpheus.Ricardo Wurmus2024-03-14
| | | | | | | * gnu/packages/bioinformatics.scm (morpheus): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de> Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
generated by cgit v1.2.3 (git 2.45.2) at 2024-08-04 22:47:37 +0000