| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (r-umi4cpackage)[arguments]: Add build
phases to patch calls of bowtie2 and perl.
[inputs]: Add perl and bowtie.
[synopsis]: Remove trailing period.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
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* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
to go" to "allows going".
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* gnu/packages/bioinformatics.scm (pplacer): Add missing input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
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* gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from
here...
[native-inputs]: ...to here.
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* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
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* gnu/packages/bioinformatics.scm (circtools): New variable.
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* gnu/packages/bioinformatics.scm (bioparser): New variable.
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* gnu/packages/bioinformatics.scm (biosoup): New variable.
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* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase
'compatibility, fixing syntax quirks that are problematic with newer
toolchains.
[native-inputs]: Do not inherit.
[inherit]: Do not inherit.
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* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
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* gnu/packages/bioinformatics.scm (qtltools): New variable.
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* gnu/packages/bioinformatics.scm (gdc-client): New variable.
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* gnu/packages/bioinformatics.scm (r-shaman): New variable.
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* gnu/packages/bioinformatics.scm (r-misha): New variable.
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* gnu/packages/bioinformatics.scm (ciri-long): New variable.
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* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.76.
(python-biopython-1.73): New variable.
(instrain)[inputs]: Replace python-biopython with python-biopython-1.73.
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* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
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* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
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* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
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This test fails/succeeds non-deterministically.
* gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable
non-deterministic test test_get_FDR_cutoff_mean.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
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* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
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* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
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* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it.
[native-inputs]: Add automake/autoconf.
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* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
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Apply upstream patch to restore compatibility with current Stackage.
* gnu/packages/patches/ngless-unliftio.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bioinformatics.scm (ngless): Use it.
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Bump packages’ versions to the lastest Stackage or Hackage
release. Since packages are interdependent, do so in a single commit.
525 packages have been updated.
These packages have been removed, because they fail to build, have no
newer version available and no dependencies:
corrode
ghc-easytest
ghc-edisonapi
ghc-edisoncore
ghc-pandoc-types
ghc-regex-tdfa-text
These have been removed, because they are no longer required:
ghc-happy-1.19.9
ghc-prettyprinter-1.6
ghc-protolude-0.3
ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc
does not use them any more.
Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
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* gnu/packages/minetest.scm (minetest-basic-trains): New variable.
* gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input.
* gnu/packages/ci.scm (laminar): Update uglifyjs input.
* gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker
r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input.
* gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/bioinformatics.scm (r-presto): New variable.
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* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
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* gnu/packages/bioinformatics.scm (megadepth): New variable.
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* gnu/packages/bioinformatics.scm (r-catch): New variable.
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* gnu/packages/bioinformatics.scm (scregseg): New variable.
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* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
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* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
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* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
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* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
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* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
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* gnu/packages/bioinformatics.scm (python-strawc): New variable.
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* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
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* gnu/packages/bioinformatics.scm (ivar): New variable.
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* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
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* gnu/packages/bioinformatics.scm (r-spectre): New variable.
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