| Age | Commit message (Expand) | Author |
|---|
| 2021-12-05 | gnu: minimap2: Update to 2.23....* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
| Efraim Flashner |
| 2021-12-04 | gnu: pigx-sars-cov2-ww: Update to 0.0.4....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
| Ricardo Wurmus |
| 2021-12-03 | gnu: imp: Update to 2.15.0....* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
| Ricardo Wurmus |
| 2021-12-03 | gnu: python-ont-fast5-api: Update to 4.0.0....* 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.
| Ricardo Wurmus |
| 2021-12-03 | gnu: Add vbz-compression....* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
| Ricardo Wurmus |
| 2021-12-03 | gnu: ivar: Disable parallel tests....* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
| Ricardo Wurmus |
| 2021-12-03 | gnu: Remove python2-biom-format....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.
| Ricardo Wurmus |
| 2021-12-02 | gnu: ribodiff: Remove trailing #T....* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
| Ricardo Wurmus |
| 2021-12-02 | gnu: ribodiff: Disable broken test....* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
| Ricardo Wurmus |
| 2021-12-02 | gnu: khmer: Fix build with Python 3.8....* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
| Ricardo Wurmus |
| 2021-12-02 | gnu: python-biom-format: Update to 2.1.10....* 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.
| Ricardo Wurmus |
| 2021-12-02 | gnu: pardre: Update to 2.2.5....* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
| Ricardo Wurmus |
| 2021-12-02 | gnu: pardre: Use C++ bindings for MPI....* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
| Ricardo Wurmus |
| 2021-12-02 | gnu: Add python-mygene....* gnu/packages/bioinformatics.scm (python-mygene): New variable.
| Ricardo Wurmus |
| 2021-12-02 | gnu: Add python-biothings-client....* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
| Ricardo Wurmus |
| 2021-12-02 | gnu: Remove couger....This package has been moved to the Guix Past channel.
* gnu/packages/bioinformatics.scm (couger): Remove variable.
| Ricardo Wurmus |
| 2021-11-30 | gnu: r-umi4cpackage: Embed references to perl and bowtie2....* 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.
| Ricardo Wurmus |
| 2021-11-20 | gnu: pigx-bsseq: Update to 0.1.6....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
| Ricardo Wurmus |
| 2021-11-18 | gnu: qtltools: Fix typo....* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
to go" to "allows going".
| Vagrant Cascadian |
| 2021-11-16 | gnu: pplacer: Fix build....* gnu/packages/bioinformatics.scm (pplacer): Add missing input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Julien Lepiller |
| 2021-11-15 | gnu: python-scanpy: Run tests conditionally....* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
| Ricardo Wurmus |
| 2021-11-11 | gnu: ciri-long: Move Cython to native inputs....* gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from
here...
[native-inputs]: ...to here.
| Ricardo Wurmus |
| 2021-11-11 | gnu: ciri-long: Fix reference to ccs....* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
| Ricardo Wurmus |
| 2021-11-11 | gnu: Add circtools....* gnu/packages/bioinformatics.scm (circtools): New variable.
| Ricardo Wurmus |
| 2021-11-11 | gnu: Add bioparser....* gnu/packages/bioinformatics.scm (bioparser): New variable.
| Ricardo Wurmus |
| 2021-11-11 | gnu: Add biosoup....* gnu/packages/bioinformatics.scm (biosoup): New variable.
| Ricardo Wurmus |
| 2021-11-03 | gnu: bedtools-2.18: Fix build with newer toolchain....* 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.
| Ricardo Wurmus |
| 2021-10-24 | gnu: Add r-umi4cpackage....* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
| Ricardo Wurmus |
| 2021-10-22 | gnu: Add qtltools....* gnu/packages/bioinformatics.scm (qtltools): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add gdc-client....* gnu/packages/bioinformatics.scm (gdc-client): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add r-shaman....* gnu/packages/bioinformatics.scm (r-shaman): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add r-misha....* gnu/packages/bioinformatics.scm (r-misha): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add ciri-long....* gnu/packages/bioinformatics.scm (ciri-long): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: python-biopython: Update to 1.76....* 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.
| Ricardo Wurmus |
| 2021-10-21 | gnu: instrain: Update to 1.5.4....* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add python-bwapy....* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add python-pyspoa....* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
| Ricardo Wurmus |
| 2021-10-12 | gnu: clipper: Disable non-deterministic test....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>
| Felix Gruber |
| 2021-10-08 | gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-chipseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-bsseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: ngless: Fix build....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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: Update Haskell ecosystem....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>
| Lars-Dominik Braun |
| 2021-09-29 | gnu: pigx-chipseq: Update to 0.0.53....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
| Ricardo Wurmus |
| 2021-09-22 | gnu: Update some packages using old JavaScript minifier....* 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>
| Charles |
| 2021-09-20 | gnu: Add r-presto....* gnu/packages/bioinformatics.scm (r-presto): New variable.
| zimoun |
| 2021-09-13 | gnu: discrover: Update package name in texlive-union....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
| Ricardo Wurmus |
| 2021-09-06 | gnu: Add megadepth....* gnu/packages/bioinformatics.scm (megadepth): New variable.
| Ricardo Wurmus |
