| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | 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 | 2021-10-12 | 1 | -1/+8 |
| * | 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 | 1 | -1/+11 |
| * | 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 | 1 | -2/+8 |
| * | 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 | 1 | -4/+12 |
| * | 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 | 1 | -1/+11 |
| * | 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 | 1 | -2/+8 |
| * | 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 | 1 | -1/+2 |
| * | 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 | 2021-10-08 | 1 | -9/+42 |
| * | 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 | 2021-09-29 | 1 | -2/+3 |
| * | 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 | 2021-09-22 | 1 | -3/+3 |
| * | gnu: Add r-presto.•••* gnu/packages/bioinformatics.scm (r-presto): New variable.
| zimoun | 2021-09-20 | 1 | -0/+34 |
| * | gnu: discrover: Update package name in texlive-union.•••* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
| Ricardo Wurmus | 2021-09-13 | 1 | -1/+1 |
| * | gnu: Add megadepth.•••* gnu/packages/bioinformatics.scm (megadepth): New variable.
| Ricardo Wurmus | 2021-09-06 | 1 | -0/+65 |
| * | gnu: Add r-catch.•••* gnu/packages/bioinformatics.scm (r-catch): New variable.
| Ricardo Wurmus | 2021-09-01 | 1 | -0/+28 |
| * | gnu: Add scregseg.•••* gnu/packages/bioinformatics.scm (scregseg): New variable.
| Ricardo Wurmus | 2021-08-31 | 1 | -0/+50 |
| * | gnu: python-strawc: Propagate pybind11.•••* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus | 2021-08-31 | 1 | -1/+2 |
| * | gnu: python-scanpy: Propagate sinfo.•••* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus | 2021-08-31 | 1 | -2/+2 |
| * | gnu: Add python-coolbox.•••* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
| Ricardo Wurmus | 2021-08-30 | 1 | -0/+49 |
| * | gnu: python-scanpy: Update to 1.8.1.•••* 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.
| Ricardo Wurmus | 2021-08-30 | 1 | -15/+48 |
| * | gnu: Add python-dna-features-viewer.•••* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
| Ricardo Wurmus | 2021-08-30 | 1 | -0/+24 |
| * | gnu: Add python-pybbi.•••* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
| Ricardo Wurmus | 2021-08-30 | 1 | -0/+47 |
| * | gnu: Add python-strawc.•••* gnu/packages/bioinformatics.scm (python-strawc): New variable.
| Ricardo Wurmus | 2021-08-27 | 1 | -0/+22 |
| * | gnu: Add r-cytonorm.•••* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
| Ricardo Wurmus | 2021-08-27 | 1 | -0/+39 |
| * | gnu: Add ivar.•••* gnu/packages/bioinformatics.scm (ivar): New variable.
| Ricardo Wurmus | 2021-08-25 | 1 | -0/+26 |
| * | gnu: fastp: Update to 0.20.1.•••* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
| Ricardo Wurmus | 2021-08-20 | 1 | -5/+4 |
| * | gnu: pigx-rnaseq: Update to 0.0.19.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
| Ricardo Wurmus | 2021-08-13 | 1 | -2/+2 |
| * | gnu: pigx-rnaseq: Update to 0.0.18.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
| Ricardo Wurmus | 2021-08-11 | 1 | -2/+2 |
| * | gnu: pigx-sars-cov2-ww: Update to 0.0.3.•••* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
| Ricardo Wurmus | 2021-08-05 | 1 | -2/+2 |
| * | gnu: Add r-spectre.•••* gnu/packages/bioinformatics.scm (r-spectre): New variable.
| Ricardo Wurmus | 2021-08-03 | 1 | -0/+72 |
| * | gnu: Add seqan 3.•••* 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.
| Ricardo Wurmus | 2021-07-26 | 1 | -11/+35 |
| * | gnu: Add segemehl.•••* gnu/packages/bioinformatics.scm (segemehl): New variable.
| Ricardo Wurmus | 2021-07-26 | 1 | -0/+48 |
| * | gnu: python-pysam: Make the check phase honor the tests? argument.•••* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
| Efraim Flashner | 2021-07-22 | 1 | -15/+16 |
| * | gnu: python-pysam: Update to 0.16.0.1.•••* 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.
| Efraim Flashner | 2021-07-22 | 1 | -25/+26 |
| * | gnu: Add htslib-1.10.•••* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
| Efraim Flashner | 2021-07-22 | 1 | -0/+13 |
| * | gnu: python-biopython: Update to 1.73.•••* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
| Efraim Flashner | 2021-07-22 | 1 | -2/+2 |
| * | gnu: Add r-battenberg.•••* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
| Lars-Dominik Braun | 2021-07-21 | 1 | -0/+30 |
| * | gnu: Add r-ascat.•••* gnu/packages/bioinformatics.scm (r-ascat): New variable.
| Lars-Dominik Braun | 2021-07-21 | 1 | -0/+29 |
| * | gnu: Add nanosv.•••* gnu/packages/bioinformatics.scm (nanosv): New variable.
| Lars-Dominik Braun | 2021-07-21 | 1 | -0/+23 |
| * | gnu: Add python-pyvcf.•••* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
| Lars-Dominik Braun | 2021-07-21 | 1 | -0/+37 |
| * | gnu: checkm: Rename and update to 1.1.3.•••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.
| Lars-Dominik Braun | 2021-07-21 | 1 | -13/+20 |
| * | gnu: Add tombo.•••* gnu/packages/bioinformatics.scm (tombo): New variable.
| Lars-Dominik Braun | 2021-07-21 | 1 | -0/+33 |
| * | gnu: Add ocaml-sqlite3.•••* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
(ocaml4.07-sqlite3): Inherit from ocaml-sqlite3.
* gnu/packages/bioinformatics.scm (pplacer): Also use package-with-ocaml4.07
with ocaml-sqlite3.
| Julien Lepiller | 2021-07-05 | 1 | -1/+1 |
| * | gnu: bioperl-minimal: Avoid top-level cross-module references.•••This could lead to circular reference breakage.
* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
| Ludovic Courtès | 2021-07-01 | 1 | -54/+55 |
| * | gnu: Do not import (gnu packages commencement).•••Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64.
* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
| Ludovic Courtès | 2021-07-01 | 1 | -1/+0 |
| * | gnu: ensembl-vep: Use a source file-name.•••* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
| Efraim Flashner | 2021-06-22 | 1 | -0/+1 |
| * | gnu: Add perl-cworld-dekker.•••* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
| Ricardo Wurmus | 2021-06-22 | 1 | -0/+94 |
| * | gnu: Add python-iced.•••* gnu/packages/bioinformatics.scm (python-iced): New variable.
| Ricardo Wurmus | 2021-06-21 | 1 | -0/+24 |
| * | gnu: Add python-cgatcore.•••* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
| Ricardo Wurmus | 2021-06-14 | 1 | -0/+59 |
| * | gnu: Rename qtbase to qtbase-5.•••This change was automated via the following command:
$ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g'
$ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g'
$ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g'
$ git checkout etc # to clear some spurious changes
This is done so the qtbase package can be upgraded to version 6 in the
following commit.
| Maxim Cournoyer | 2021-06-14 | 1 | -1/+1 |
| * | gnu: pigx-sars-cov2-ww: Update to 0.0.2.•••* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
| Ricardo Wurmus | 2021-06-08 | 1 | -3/+4 |
