summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
AgeCommit message (Expand)Author
2023-02-09gnu: Add python-scrublet....* gnu/packages/bioinformatics.scm (python-scrublet): New variable. Navid Afkhami
2023-02-07gnu: Add bitmapperbs....* gnu/packages/bioinformatics.scm (bitmapperbs): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-02-07Revert "gnu: Add bitmapperbs."...This reverts commit f55cc9cb0fb6c5dd56196009681e042c1aef415d. This commit was prematurely pushed. Ricardo Wurmus
2023-02-07gnu: Add bitmapperbs....* gnu/packages/bioinformatics.scm (bitmapperbs): New variable. Navid Afkhami
2023-02-06gnu: Add r-ggsankey....* gnu/packages/bioinformatics.scm (r-ggsankey): New variable. Ricardo Wurmus
2023-02-03gnu: Add r-psupertime....* gnu/packages/bioinformatics.scm (r-psupertime): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-02-03gnu: Add python-demuxem....* gnu/packages/bioinformatics.scm (python-demuxem): New variable. Navid Afkhami
2023-02-03gnu: Add python-pegasusio....* gnu/packages/bioinformatics.scm (python-pegasusio): New variable. Navid Afkhami
2023-02-03gnu: Add r-streamgraph....* gnu/packages/bioinformatics.scm (r-streamgraph): New variable. Navid Afkhami
2023-01-25gnu: gdcm: Add documentation....* gnu/packages/bioinformatics.scm (gdcm)[outputs]: New field. [arguments]: Add #:phases. Augment #:configure-flags. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Tor-björn Claesson
2023-01-25gnu: gdcm: Ignore 3 failing tests....* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more failing tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Tor-björn Claesson
2023-01-25gnu: Add python-slamdunk....* gnu/packages/bioinformatics.scm (python-slamdunk): New variable. Ricardo Wurmus
2023-01-25gnu: Add python-phylophlan....* gnu/packages/bioinformatics.scm (python-phylophlan): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>. Mădălin Ionel Patrașcu
2023-01-25gnu: Add python-hclust2....* gnu/packages/bioinformatics.scm (python-hclust2): New variable. Mădălin Ionel Patrașcu
2023-01-25gnu: Add python-cmseq....* gnu/packages/bioinformatics.scm (python-cmseq): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>. Mădălin Ionel Patrașcu
2023-01-25gnu: Add python-bcbio-gff/biopython-1.73....* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable. Ricardo Wurmus
2023-01-20gnu: Add r-tsis....* gnu/packages/bioinformatics.scm (r-tsis): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-01-20gnu: Add r-doubletcollection....* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-01-20gnu: Add python-vireosnp....* gnu/packages/bioinformatics.scm (python-vireosnp): New variable. Simon Tournier
2023-01-15gnu: gdcm: Fix recursive Git source hash....The hash being used covered only the gdcm repository, not the gdcmdata submodule. * gnu/packages/bioinformatics.scm (gdcm)[source]: Update hash. Reported by civodul in #guix. Tobias Geerinckx-Rice
2023-01-17gnu: gdcm: Update to 3.0.20....* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20. [home-page, license]: Update. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Tor-björn Claesson
2023-01-16gnu: r-cytonorm: Update to 0.0.10-1.166f9ff....* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff. Ricardo Wurmus
2023-01-13gnu: r-signac: Update to 1.9.0-1.af41427....* gnu/packages/bioinformatics.scm (r-signac): Update to 1.9.0-1.af41427. [propagated-inputs]: Remove r-ggforce, r-ggrepel, r-ggseqlogo, r-lsa, r-qlcmatrix, and r-seurat; add r-vctrs. Ricardo Wurmus
2023-01-13gnu: python-cellbender: Update source hash....The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52 to d92cfc5a55c8b1771348468035993c52df975170. * gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update. Marius Bakke
2023-01-12gnu: Add cellsnp-lite....* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable. Simon Tournier
2023-01-09gnu: Add r-gg3d....* gnu/packages/bioinformatics.scm (r-gg3d): New variable. Ricardo Wurmus
2023-01-08gnu: Move Java XML packages to new module....* gnu/packages/xml.scm (java-simple-xml, java-jaxp, java-apache-xml-commons-resolver, java-jaxen, java-xom, java-xsdlib, java-xpp3, java-xmlpull2, java-xmlpull-api-v1, java-dom4j, java-kxml2, java-stax, java-jettison, java-jdom2, java-xstream, java-mxparser): Move these variables from here... * gnu/packages/java-xml.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Register new file. * gnu/packages/axoloti.scm, gnu/packages/batik.scm, gnu/packages/bioinformatics.scm, gnu/packages/groovy.scm, gnu/packages/java.scm, gnu/packages/maven.scm: Adjust module imports. Ricardo Wurmus
2023-01-08gnu: Add gdcm....* gnu/packages/bioinformatics.scm (gdcm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Antero Mejr
2023-01-07gnu: Use old setuptools in packages that relies on use_2to3 conversion....This fixes a regression since 520cdf80581669646ff61e9f18f3b27045556e76 where the use_2to3 functionality was removed from setuptools. * gnu/packages/graph.scm (python-louvain)[native-inputs]: Change from PYTHON-SETUPTOOLS to PYTHON-SETUPTOOLS-57. * gnu/packages/python-check.scm (python-parameterizedtestcase)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-anyjson)[native-inputs]: Add PYTHON-SETUPTOOLS-57. * gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Change from PYTHON-SETUPTOOLS-FOR-TENSORFLOW to PYTHON-SETUPTOOLS-57. Marius Bakke
2023-01-06gnu: bbmap: Update to 39.01....* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01. Ricardo Wurmus
2023-01-06gnu: bbmap: Use gexp....* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp. Ricardo Wurmus
2023-01-06gnu: nanopolish: Drop input labels....* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels. Ricardo Wurmus
2023-01-06gnu: nanopolish: Update to 0.14.0....* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0. [source]: Update snippet. [arguments]: Use gexp; use cc-for-target; drop #T from build phases. [inputs]: Add minimap2. [native-inputs]: Add cmake-minimal. Ricardo Wurmus
2023-01-06gnu: filtlong: Use Python 3....* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with python-wrapper. Ricardo Wurmus
2023-01-06gnu: filtlong: Use gexp....* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp. Ricardo Wurmus
2023-01-06gnu: filtlong: Drop input labels....* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels. Ricardo Wurmus
2023-01-06gnu: filtlong: Remove trailing #T from build phases....* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T. Ricardo Wurmus
2023-01-06gnu: ngless: Use gexp....* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp. Ricardo Wurmus
2023-01-06gnu: ngless: Remove trailing #T from build phases....* gnu/packages/bioinformatics.scm (ngless)[arguments]: Remove trailing #T. Ricardo Wurmus
2023-01-04gnu: bamtools: Build shared libraries....* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared libraries instead of static libs. Ricardo Wurmus
2023-01-04gnu: Add scallop....* gnu/packages/bioinformatics.scm (scallop): New variable. Ricardo Wurmus
2023-01-03gnu: Add python-bcbio-gff....* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable. Ricardo Wurmus
2022-12-30gnu: Add r-domultibarheatmap....* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable. Ricardo Wurmus
2022-12-28gnu: r-giotto: Update to 1.1.2-1.3c8067c....* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c. Ricardo Wurmus
2022-12-22gnu: Add r-bedtorch....* gnu/packages/bioinformatics.scm (r-bedtorch): New variable. Ricardo Wurmus
2022-12-22gnu: Add r-rhtslib12....* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable. Ricardo Wurmus
2022-12-22gnu: Add wiggletools....* gnu/packages/bioinformatics.scm (wiggletools): New variable. Ricardo Wurmus
2022-12-22gnu: Add python-episcanpy....* gnu/packages/bioinformatics.scm (python-episcanpy): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2022-12-22gnu: Add python-bamnostic....* gnu/packages/bioinformatics.scm (python-bamnostic): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2022-12-21gnu: Add vembrane....* gnu/packages/bioinformatics.scm (vembrane): New variable. Ricardo Wurmus
generated by cgit v1.2.3 (git 2.46.2) at 2024-10-22 02:57:55 +0000