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* gnu: python-ont-fast5-api: Update to 4.0.0.Ricardo Wurmus2021-12-03
| | | | | | | | * gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0. [source]: Remove bundled plugin binaries. [arguments]: Install plugin from inputs. [inputs]: Add vbz-compression. [propagated-inputs]: Remove python-six; add python-packaging.
* gnu: Add vbz-compression.Ricardo Wurmus2021-12-03
| | | | * gnu/packages/bioinformatics.scm (vbz-compression): New variable.
* gnu: ivar: Disable parallel tests.Ricardo Wurmus2021-12-03
| | | | * gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
* gnu: Remove python2-biom-format.Ricardo Wurmus2021-12-03
| | | | | | | | There are no users of this variant, and the current version of biom-format does not support Python 2. * gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable. (python-biom-format)[properties]: Remove field.
* gnu: ribodiff: Remove trailing #T.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase.
* gnu: ribodiff: Disable broken test.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test.
* gnu: khmer: Fix build with Python 3.8.Ricardo Wurmus2021-12-02
| | | | | | * gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T. [arguments]: Remove trailing #T from build phases; add build phase 'python-3.8-compatibility.
* gnu: python-biom-format: Update to 2.1.10.Ricardo Wurmus2021-12-02
| | | | | | | | * gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10. [source]: Simplify snippet. [arguments]: Add phase 'relax; remove trailing #T from other build phases. [propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with python-pandas.
* gnu: pardre: Update to 2.2.5.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5. [arguments]: Remove trailing #T and update comment about tests.
* gnu: pardre: Use C++ bindings for MPI.Ricardo Wurmus2021-12-02
| | | | | * gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with openmpi-c++.
* gnu: Add python-mygene.Ricardo Wurmus2021-12-02
| | | | * gnu/packages/bioinformatics.scm (python-mygene): New variable.
* gnu: Add python-biothings-client.Ricardo Wurmus2021-12-02
| | | | * gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
* gnu: Remove couger.Ricardo Wurmus2021-12-02
| | | | | | This package has been moved to the Guix Past channel. * gnu/packages/bioinformatics.scm (couger): Remove variable.
* gnu: r-umi4cpackage: Embed references to perl and bowtie2.Ricardo Wurmus2021-11-30
| | | | | | | * 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.
* gnu: pigx-bsseq: Update to 0.1.6.Ricardo Wurmus2021-11-20
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
* gnu: qtltools: Fix typo.Vagrant Cascadian2021-11-18
| | | | | * gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows to go" to "allows going".
* gnu: pplacer: Fix build.Julien Lepiller2021-11-16
| | | | | | * gnu/packages/bioinformatics.scm (pplacer): Add missing input. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: python-scanpy: Run tests conditionally.Ricardo Wurmus2021-11-15
| | | | | * gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS? argument.
* gnu: ciri-long: Move Cython to native inputs.Ricardo Wurmus2021-11-11
| | | | | | * gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from here... [native-inputs]: ...to here.
* gnu: ciri-long: Fix reference to ccs.Ricardo Wurmus2021-11-11
| | | | | | * gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase "fix-reference-to-ccs". [inputs]: Add circtools.
* gnu: Add circtools.Ricardo Wurmus2021-11-11
| | | | * gnu/packages/bioinformatics.scm (circtools): New variable.
* gnu: Add bioparser.Ricardo Wurmus2021-11-11
| | | | * gnu/packages/bioinformatics.scm (bioparser): New variable.
* gnu: Add biosoup.Ricardo Wurmus2021-11-11
| | | | * gnu/packages/bioinformatics.scm (biosoup): New variable.
* gnu: bedtools-2.18: Fix build with newer toolchain.Ricardo Wurmus2021-11-03
| | | | | | | | * 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.
* gnu: Add r-umi4cpackage.Ricardo Wurmus2021-10-24
| | | | * gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
* gnu: Add qtltools.Ricardo Wurmus2021-10-22
| | | | * gnu/packages/bioinformatics.scm (qtltools): New variable.
* gnu: Add gdc-client.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (gdc-client): New variable.
* gnu: Add r-shaman.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (r-shaman): New variable.
* gnu: Add r-misha.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (r-misha): New variable.
* gnu: Add ciri-long.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (ciri-long): New variable.
* gnu: python-biopython: Update to 1.76.Ricardo Wurmus2021-10-21
| | | | | | * 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.
* gnu: instrain: Update to 1.5.4.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
* gnu: Add python-bwapy.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (python-bwapy): New variable.
* gnu: Add python-pyspoa.Ricardo Wurmus2021-10-21
| | | | * gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
* gnu: clipper: Disable non-deterministic test.Felix Gruber2021-10-12
| | | | | | | | | 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>
* gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | * 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.
* gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | * 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.
* gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | * 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.
* gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | * 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.
* gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun2021-10-08
| | | | | | | * 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.
* gnu: ngless: Fix build.Lars-Dominik Braun2021-10-08
| | | | | | | | 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.
* gnu: Update Haskell ecosystem.Lars-Dominik Braun2021-10-08
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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>
* gnu: pigx-chipseq: Update to 0.0.53.Ricardo Wurmus2021-09-29
| | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53. [inputs]: Add r-hexbin.
* gnu: Update some packages using old JavaScript minifier.Charles2021-09-22
| | | | | | | | | | | * 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>
* gnu: Add r-presto.zimoun2021-09-20
| | | | * gnu/packages/bioinformatics.scm (r-presto): New variable.
* gnu: discrover: Update package name in texlive-union.Ricardo Wurmus2021-09-13
| | | | | * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace texlive-fonts-cm with texlive-cm.
* gnu: Add megadepth.Ricardo Wurmus2021-09-06
| | | | * gnu/packages/bioinformatics.scm (megadepth): New variable.
* gnu: Add r-catch.Ricardo Wurmus2021-09-01
| | | | * gnu/packages/bioinformatics.scm (r-catch): New variable.
* gnu: Add scregseg.Ricardo Wurmus2021-08-31
| | | | * gnu/packages/bioinformatics.scm (scregseg): New variable.
* gnu: python-strawc: Propagate pybind11.Ricardo Wurmus2021-08-31
| | | | | | * gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from here... [propagated-inputs]: ...to here.
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