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* gnu: bandage: Do not yet use the 'imagemagick/stable' variant.Maxime Devos2024-08-31
| | | | | | | | | | | | | | | Once <https://issues.guix.gnu.org/47475> (‘Closure of bandage is way too large’) has been fixed, the variant will probably be usable. * gnu/packages/bioinformatics.scm (bandage): [arguments]<#:disallowed-references>: Once the issue has been fixed, prevent the imagemagick/stable package from ending up in the closure. [native-inputs]: Note that 'imagemagick/stable' cannot be used yet. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Change-Id: Ie13100eb424b14971055ff91db49bc7029cb6168
* gnu: flair: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (flair) [inputs]: Add bash-minimal. Change-Id: I66fd550c617430ebbede36e140ee48df1c6149ca
* gnu: ccwl: Remove input labels.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (ccwl) [inputs]: Remove input labels. Change-Id: Ie00325f7472524a0c8431b98ca6172a2f7f7096a
* gnu: arriba: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (arriba) [inputs]: Add bash-minimal. Change-Id: Ib30f9e0872dc24ca24e498eba51560c750e75d22
* gnu: nanopolish: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (nanopolish) [inputs]: Add bash-minimal. Change-Id: Ie9cbe808e1ae678fb56db03537721f43da3c2b4c
* gnu: filtlong: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (filtlong) [inputs]: Add bash-minimal. Change-Id: I8a4b402d66a06a27c9cc8abacdefecd251c2095c
* gnu: ngless: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (ngless) [inputs]: Add bash-minimal. Change-Id: I3560d4f10261f87c819bd12cf0956a6cf77324cb
* gnu: rcas-web: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Add bash-minimal. Change-Id: I71f0e435e969e0a689caea90d9f442929c7d9431
* gnu: shorah: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (shorah) [inputs]: Add bash-minimal. Change-Id: Ibe428a0ec32a5acf7e70269376aaf16e97507d51
* gnu: rsem: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (rsem) [inputs]: Add bash-minimal. Change-Id: Idd9fbf729e9bcdd009cf517ec23064544bdf6f43
* gnu: roary: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (roary): Delete trailing #t. [inputs]: Add bash-minimal. Remove labels. Change-Id: Id5ea1b12e2fa641d96a762f5f3b89edbd43a4ffa
* gnu: proteinortho: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (proteinortho)[inputs]: Add bash-minimal. Remove labels. Change-Id: I74e243d598a544a9a58ea77a229b6a2b2f56c5b2
* gnu: mafft: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (mafft): Delete trailing #t. [inputs]: Add bash-minimal. Change-Id: Id30d22dc37ee57591f17dc116de81500b09adf3c
* gnu: edirect: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (edirect): Delete trailing #t. [inputs]: Add bash-minimal. Change-Id: I28474c3ec5866b5e9f824d5d71e6cc8be5791f58
* gnu: repeat-masker: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (repeat-masker) [inputs]: Add bash-minimal. Change-Id: I81d4806cc65eed8040824cb72d6c462c8762294e
* gnu: bioperl-minimal: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (bioperl-minimal) [inputs]: Add bash-minimal. Change-Id: I274572a2e87f63afcca2e433454a71f078291a06
* gnu: ribotaper: Add bash-minimal to inputs.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (ribotaper) [inputs]: Add bash-minimal. Change-Id: I5adc841c15c054101d32f30579a89aa7290c6f3c
* gnu: ccwl: Import the correct set of modules.Maxim Cournoyer2024-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (ccwl) [arguments] <modules>: Replace %default-gnu-imported-modules with %default-gnu-modules. Change-Id: I9c96e847de537b11bc8396d6c0e7968a1a9f3e98
* build-systems: gnu: Export %default-gnu-imported-modules and ↵Maxim Cournoyer2024-08-31
| | | | | | | | | | | | | | | | | | | | | %default-gnu-modules. Until now users would have to cargo cult or inspect the private %default-modules variable of (guix build-systems gnu) to discover which modules to include when extending the used modules via the #:modules argument. The renaming was automated via the command: $ git grep -l %gnu-build-system-modules | xargs sed 's/%gnu-build-system-modules/%default-gnu-imported-modules/' -i * guix/build-system/gnu.scm (%gnu-build-system-modules): Rename to... (%default-gnu-imported-modules): ... this. (%default-modules): Rename to... (%default-gnu-modules): ... this. Export. (dist-package, gnu-build, gnu-cross-build): Adjust accordingly. Change-Id: Idef307fff13cb76f3182d782b26e1cd3a5c757ee
* gnu: gdcm: Build manpages.Bruno Victal2024-08-31
| | | | | | | | * gnu/packages/bioinformatics.scm (gdcm)[arguments]<#:configure-flags>: Re-enable manpages. [native-inputs]: Add libxslt. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
* gnu: bwa,bwa-pssm: Improve package style.Zheng Junjie2024-07-30
| | | | | | | * gnu/packages/bioinformatics.scm (bwa)[arguments]: Use G-expression. (bwa-pssm)[arguments]: Use G-expression. Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
* gnu: bwa: Fix cross-compiling.Zheng Junjie2024-07-30
| | | | | | | * gnu/packages/bioinformatics.scm (bwa)[arguments]<#:make-flags>: Use CC-FOR-TARGET. Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
* gnu: bwa: Update to 0.7.18.Spencer King2024-07-30
| | | | | | | | * gnu/packages/bioinformatics.scm (bwa): Update to 0.7.18. [source]: Switch to git-fetch. [supported-systems]: Add aarch64-linux. Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
* gnu: Add python-muon.guix@mawumag.com2024-07-01
| | | | | | | * gnu/packages/bioinformatics.scm (python-muon): New variable. Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add python-mofapy2.guix@mawumag.com2024-07-01
| | | | | | | * gnu/packages/bioinformatics.scm (python-mofapy2): New variable. Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-anpan.Afkhami, Navid2024-07-01
| | | | | | | * gnu/packages/bioinformatics.scm (r-anpan): New variable. Change-Id: Ia01ba3be7424306674b9c9b2904f1f0cfa66d818 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-cmdstanr.Afkhami, Navid2024-06-30
| | | | | | | * gnu/packages/bioinformatics.scm (r-cmdstanr): New variable. Change-Id: Ic9e83486f7ab7f0e7075343af630c4dcecf597b5 Signed-off-by: Andreas Enge <andreas@enge.fr>
* gnu: jellyfish: Enable building on all 64bit platforms.Efraim Flashner2024-06-30
| | | | | | | * gnu/packages/bioinformatics.scm (jellyfish)[supported-systems]: Mark all 64bit platforms as supported. Change-Id: Ia79d8052bf6ff347422e4b1ce38dc379d45a9be6
* gnu: Add r-rphyloxml.Afkhami, Navid2024-06-28
| | | | | | | * gnu/packages/bioinformatics.scm (r-rphyloxml): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I5b799986064f2af5fe74454f2e78fea7d9947260
* gnu: Add r-rnacrosslinkoo.Afkhami, Navid2024-06-28
| | | | | | * gnu/packages/bioinformatics.scm (r-rnacrosslinkoo): New variable. Change-Id: I1ca6dcef9c093627c3743d1176e587cf40053ba0
* 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>
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