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2021-10-24gnu: Add r-umi4cpackage.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
2021-10-22gnu: Add qtltools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (qtltools): New variable.
2021-10-21gnu: Add gdc-client.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
2021-10-21gnu: Add r-shaman.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
2021-10-21gnu: Add r-misha.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-misha): New variable.
2021-10-21gnu: Add ciri-long.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
2021-10-21gnu: python-biopython: Update to 1.76.Ricardo Wurmus
* 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.
2021-10-21gnu: instrain: Update to 1.5.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
2021-10-21gnu: Add python-bwapy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
2021-10-21gnu: Add python-pyspoa.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
2021-10-12gnu: clipper: Disable non-deterministic test.Felix Gruber
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>
2021-10-08gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* 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.
2021-10-08gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* 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.
2021-10-08gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* 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.
2021-10-08gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* 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.
2021-10-08gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* 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.
2021-10-08gnu: ngless: Fix build.Lars-Dominik Braun
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.
2021-10-08gnu: Update Haskell ecosystem.Lars-Dominik Braun
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>
2021-09-29gnu: pigx-chipseq: Update to 0.0.53.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53. [inputs]: Add r-hexbin.
2021-09-22gnu: Update some packages using old JavaScript minifier.Charles
* 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>
2021-09-20gnu: Add r-presto.zimoun
* gnu/packages/bioinformatics.scm (r-presto): New variable.
2021-09-13gnu: discrover: Update package name in texlive-union.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace texlive-fonts-cm with texlive-cm.
2021-09-06gnu: Add megadepth.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (megadepth): New variable.
2021-09-01gnu: Add r-catch.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-catch): New variable.
2021-08-31gnu: Add scregseg.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scregseg): New variable.
2021-08-31gnu: python-strawc: Propagate pybind11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from here... [propagated-inputs]: ...to here.
2021-08-31gnu: python-scanpy: Propagate sinfo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move python-sinfo from here... [propagated-inputs]: ...to here.
2021-08-30gnu: Add python-coolbox.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
2021-08-30gnu: python-scanpy: Update to 1.8.1.Ricardo Wurmus
* 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.
2021-08-30gnu: Add python-dna-features-viewer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
2021-08-30gnu: Add python-pybbi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
2021-08-27gnu: Add python-strawc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
2021-08-27gnu: Add r-cytonorm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
2021-08-25gnu: Add ivar.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ivar): New variable.
2021-08-20gnu: fastp: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1. [arguments]: Set PREFIX instead of BINDIR.
2021-08-13gnu: pigx-rnaseq: Update to 0.0.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
2021-08-11gnu: pigx-rnaseq: Update to 0.0.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
2021-08-05gnu: pigx-sars-cov2-ww: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
2021-08-03gnu: Add r-spectre.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
2021-07-26gnu: Add seqan 3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqan): Rename this variable... (seqan-2): ...to this. (seqan): New variable for seqan3. (flexbar)[native-inputs]: Update name for seqan 2.
2021-07-26gnu: Add segemehl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (segemehl): New variable.
2021-07-22gnu: python-pysam: Make the check phase honor the tests? argument.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f.
2021-07-22gnu: python-pysam: Update to 0.16.0.1.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Replace htslib-1.9 with 1.10. [native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10, bcftools-1.9 with 1.10. (bcftools-1.9): Replace with bcftools-1.10. [native-inputs]: Replace htslib-1.9 with 1.10. (samtools-1.9): Replace with samtools-1.10. [inputs]: Replace htslib-1.9 with 1.10.
2021-07-22gnu: Add htslib-1.10.Efraim Flashner
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22gnu: python-biopython: Update to 1.73.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
2021-07-21gnu: Add r-battenberg.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21gnu: Add r-ascat.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
2021-07-21gnu: Add nanosv.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (nanosv): New variable.
2021-07-21gnu: Add python-pyvcf.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
2021-07-21gnu: checkm: Rename and update to 1.1.3.Lars-Dominik Braun
Renamed from python2-checkm-genome to checkm to better reflect its status as standalone-application and support for Python 3. * gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to… (checkm): …here and update to 1.1.3. [propagated-inputs]: Move to inputs. [inputs]: Use Python 3 dependencies. [home-page]: Point to real home-page.
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