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2023-02-16gnu: Remove unneeded module imports.Efraim Flashner
* gnu/packages/abiword.scm, * gnu/packages/ada.scm, * gnu/packages/agda.scm, * gnu/packages/backup.scm, * gnu/packages/barrier.scm, * gnu/packages/bioinformatics.scm, * gnu/packages/bootstrap.scm, * gnu/packages/bqn.scm, * gnu/packages/c.scm, * gnu/packages/chemistry.scm, * gnu/packages/coq.scm, * gnu/packages/cross-base.scm, * gnu/packages/databases.scm, * gnu/packages/emacs-xyz.scm, * gnu/packages/enlightenment.scm, * gnu/packages/games.scm, * gnu/packages/geo.scm, * gnu/packages/ghostscript.scm, * gnu/packages/gl.scm, * gnu/packages/golang.scm, * gnu/packages/jami.scm, * gnu/packages/java-maths.scm, * gnu/packages/kde-frameworks.scm, * gnu/packages/kde-plasma.scm, * gnu/packages/language.scm, * gnu/packages/libreoffice.scm, * gnu/packages/linphone.scm, * gnu/packages/lisp.scm, * gnu/packages/llvm.scm, * gnu/packages/machine-learning.scm, * gnu/packages/minetest.scm, * gnu/packages/monitoring.scm, * gnu/packages/nfs.scm, * gnu/packages/ocr.scm, * gnu/packages/opencl.scm, * gnu/packages/pdf.scm, * gnu/packages/python-xyz.scm, * gnu/packages/racket.scm, * gnu/packages/rust.scm, * gnu/packages/syncthing.scm, * gnu/packages/syndication.scm, * gnu/packages/telegram.scm, * gnu/packages/vulkan.scm, * gnu/packages/web-browsers.scm, * gnu/packages/web.scm, * gnu/packages/webkit.scm: Remove some unecessary module imports.
2023-02-16gnu: fastqc: Update to 0.11.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastqc): Update to 0.11.9. [source]: Fetch via git; delete bundled jar files. [arguments]: Also patch .classpath file in 'fix-dependencies; fix patching of reference to java in fastqc wrapper; override CLASSPATH.
2023-02-13gnu: jellyfish: Remove confusing quoting syntax.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Do not mix quasiquote with gexp.
2023-02-13gnu: jellyfish: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Drop package labels.
2023-02-13gnu: fastp: Update to 0.23.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastp): Update to 0.23.2. [inputs]: Remove zlib; add isa-l and libdeflate.
2023-02-13gnu: fastp: Simplify.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Simplify gexp.
2023-02-13gnu: fastqc: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastqc)[arguments]: Use gexp; drop trailing #T from build phase. [inputs]: Drop package labels.
2023-02-11gnu: go-github-com-biogo-hts-bam: Update to 1.4.4.Efraim Flashner
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): Update to 1.4.4.
2023-02-10gnu: scregseg: Update to 0.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scregseg): Update to 0.1.3. [source]: Simplify snippet. [build-system]: Use pyproject-build-system. [arguments]: Add phases 'set-numba-cache-dir and 'build-extensions; enable tests.
2023-02-10gnu: Add python-doubletdetection.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-doubletdetection): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2023-02-10gnu: Add python-phenograph.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-phenograph): New variable.
2023-02-10gnu: Add louvain.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (louvain): New variable.
2023-02-09gnu: Add python-scrublet.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-scrublet): New variable.
2023-02-07gnu: Add bitmapperbs.Navid Afkhami
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-02-07Revert "gnu: Add bitmapperbs."Ricardo Wurmus
This reverts commit f55cc9cb0fb6c5dd56196009681e042c1aef415d. This commit was prematurely pushed.
2023-02-07gnu: Add bitmapperbs.Navid Afkhami
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
2023-02-06gnu: Add r-ggsankey.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggsankey): New variable.
2023-02-03gnu: Add r-psupertime.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-psupertime): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-02-03gnu: Add python-demuxem.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-demuxem): New variable.
2023-02-03gnu: Add python-pegasusio.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-pegasusio): New variable.
2023-02-03gnu: Add r-streamgraph.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-streamgraph): New variable.
2023-01-25gnu: gdcm: Add documentation.Tor-björn Claesson
* gnu/packages/bioinformatics.scm (gdcm)[outputs]: New field. [arguments]: Add #:phases. Augment #:configure-flags. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-25gnu: gdcm: Ignore 3 failing tests.Tor-björn Claesson
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more failing tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-25gnu: Add python-slamdunk.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-slamdunk): New variable.
2023-01-25gnu: Add python-phylophlan.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-phylophlan): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-01-25gnu: Add python-hclust2.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-hclust2): New variable.
2023-01-25gnu: Add python-cmseq.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-cmseq): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-01-25gnu: Add python-bcbio-gff/biopython-1.73.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable.
2023-01-20gnu: Add r-tsis.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-tsis): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-01-20gnu: Add r-doubletcollection.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-01-20gnu: Add python-vireosnp.Simon Tournier
* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
2023-01-15gnu: gdcm: Fix recursive Git source hash.Tobias Geerinckx-Rice
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.
2023-01-17gnu: gdcm: Update to 3.0.20.Tor-björn Claesson
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20. [home-page, license]: Update. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-16gnu: r-cytonorm: Update to 0.0.10-1.166f9ff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
2023-01-13gnu: r-signac: Update to 1.9.0-1.af41427.Ricardo Wurmus
* 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.
2023-01-13gnu: python-cellbender: Update source hash.Marius Bakke
The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52 to d92cfc5a55c8b1771348468035993c52df975170. * gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
2023-01-12gnu: Add cellsnp-lite.Simon Tournier
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
2023-01-09gnu: Add r-gg3d.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
2023-01-08gnu: Move Java XML packages to new module.Ricardo Wurmus
* 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.
2023-01-08gnu: Add gdcm.Antero Mejr
* gnu/packages/bioinformatics.scm (gdcm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-07gnu: Use old setuptools in packages that relies on use_2to3 conversion.Marius Bakke
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.
2023-01-06gnu: bbmap: Update to 39.01.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
2023-01-06gnu: bbmap: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
2023-01-06gnu: nanopolish: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
2023-01-06gnu: nanopolish: Update to 0.14.0.Ricardo Wurmus
* 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.
2023-01-06gnu: filtlong: Use Python 3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with python-wrapper.
2023-01-06gnu: filtlong: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
2023-01-06gnu: filtlong: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
2023-01-06gnu: filtlong: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
2023-01-06gnu: ngless: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
generated by cgit v1.2.3 (git 2.46.0) at 2024-08-22 02:43:17 +0000