Age | Commit message (Collapse) | Author |
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Do not mix
quasiquote with gexp.
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* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Drop package
labels.
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* gnu/packages/bioinformatics.scm (fastp): Update to 0.23.2.
[inputs]: Remove zlib; add isa-l and libdeflate.
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* gnu/packages/bioinformatics.scm (fastp)[arguments]: Simplify gexp.
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* gnu/packages/bioinformatics.scm (fastqc)[arguments]: Use gexp; drop
trailing #T from build phase.
[inputs]: Drop package labels.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): Update
to 1.4.4.
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* 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.
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* gnu/packages/bioinformatics.scm (python-doubletdetection): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
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* gnu/packages/bioinformatics.scm (python-phenograph): New variable.
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* gnu/packages/bioinformatics.scm (louvain): New variable.
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* gnu/packages/bioinformatics.scm (python-scrublet): New variable.
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* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
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This reverts commit f55cc9cb0fb6c5dd56196009681e042c1aef415d.
This commit was prematurely pushed.
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* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
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* gnu/packages/bioinformatics.scm (r-ggsankey): New variable.
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* gnu/packages/bioinformatics.scm (r-psupertime): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioinformatics.scm (python-demuxem): New variable.
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* gnu/packages/bioinformatics.scm (python-pegasusio): New variable.
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* gnu/packages/bioinformatics.scm (r-streamgraph): New variable.
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* gnu/packages/bioinformatics.scm (gdcm)[outputs]: New field.
[arguments]: Add #:phases. Augment #:configure-flags.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more
failing tests.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioinformatics.scm (python-slamdunk): New variable.
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* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
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* gnu/packages/bioinformatics.scm (python-hclust2): New variable.
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* gnu/packages/bioinformatics.scm (python-cmseq): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
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* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable.
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* gnu/packages/bioinformatics.scm (r-tsis): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
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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.
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* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20.
[home-page, license]: Update.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
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* 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.
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The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52
to d92cfc5a55c8b1771348468035993c52df975170.
* gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
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* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
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* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (gdcm): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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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.
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* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
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* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
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* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
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* 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.
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* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with
python-wrapper.
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* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
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* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
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* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
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