| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: pigx-bsseq: Update to 0.1.6.•••* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
| Ricardo Wurmus | 2021-11-20 | 1 | -2/+2 |
| * | gnu: qtltools: Fix typo.•••* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
to go" to "allows going".
| Vagrant Cascadian | 2021-11-18 | 1 | -1/+1 |
| * | gnu: pplacer: Fix build.•••* gnu/packages/bioinformatics.scm (pplacer): Add missing input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Julien Lepiller | 2021-11-16 | 1 | -1/+3 |
| * | gnu: python-scanpy: Run tests conditionally.•••* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
| Ricardo Wurmus | 2021-11-15 | 1 | -40/+41 |
| * | 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 | 1 | -2/+2 |
| * | 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 | 1 | -3/+14 |
| * | gnu: Add circtools.•••* gnu/packages/bioinformatics.scm (circtools): New variable.
| Ricardo Wurmus | 2021-11-11 | 1 | -0/+57 |
| * | gnu: Add bioparser.•••* gnu/packages/bioinformatics.scm (bioparser): New variable.
| Ricardo Wurmus | 2021-11-11 | 1 | -0/+36 |
| * | gnu: Add biosoup.•••* gnu/packages/bioinformatics.scm (biosoup): New variable.
| Ricardo Wurmus | 2021-11-11 | 1 | -0/+31 |
| * | 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 | 2021-11-03 | 1 | -2/+14 |
| * | gnu: Add r-umi4cpackage.•••* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
| Ricardo Wurmus | 2021-10-24 | 1 | -0/+27 |
| * | gnu: Add qtltools.•••* gnu/packages/bioinformatics.scm (qtltools): New variable.
| Ricardo Wurmus | 2021-10-22 | 1 | -0/+77 |
| * | gnu: Add gdc-client.•••* gnu/packages/bioinformatics.scm (gdc-client): New variable.
| Ricardo Wurmus | 2021-10-21 | 1 | -0/+40 |
| * | gnu: Add r-shaman.•••* gnu/packages/bioinformatics.scm (r-shaman): New variable.
| Ricardo Wurmus | 2021-10-21 | 1 | -0/+44 |
| * | gnu: Add r-misha.•••* gnu/packages/bioinformatics.scm (r-misha): New variable.
| Ricardo Wurmus | 2021-10-21 | 1 | -0/+36 |
| * | gnu: Add ciri-long.•••* gnu/packages/bioinformatics.scm (ciri-long): New variable.
| Ricardo Wurmus | 2021-10-21 | 1 | -0/+50 |
| * | 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 | 1 | -3/+15 |
| * | gnu: instrain: Update to 1.5.4.•••* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
| Ricardo Wurmus | 2021-10-21 | 1 | -2/+2 |
| * | gnu: Add python-bwapy.•••* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
| Ricardo Wurmus | 2021-10-21 | 1 | -0/+26 |
| * | gnu: Add python-pyspoa.•••* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
| Ricardo Wurmus | 2021-10-21 | 1 | -0/+47 |
| * | 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 |
