Age | Commit message (Collapse) | Author |
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* 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>
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* gnu/packages/bioinformatics.scm (r-presto): New variable.
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* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
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* gnu/packages/bioinformatics.scm (megadepth): New variable.
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* gnu/packages/bioinformatics.scm (r-catch): New variable.
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* gnu/packages/bioinformatics.scm (scregseg): New variable.
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* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
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* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
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* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
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* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
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* gnu/packages/bioinformatics.scm (python-strawc): New variable.
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* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
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* gnu/packages/bioinformatics.scm (ivar): New variable.
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* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
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* gnu/packages/bioinformatics.scm (r-spectre): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (segemehl): New variable.
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* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
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* 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.
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* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
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* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
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* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
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* gnu/packages/bioinformatics.scm (r-ascat): New variable.
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* gnu/packages/bioinformatics.scm (nanosv): New variable.
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* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
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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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* gnu/packages/bioinformatics.scm (tombo): New variable.
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* 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.
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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'.
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Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64.
* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
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* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
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* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
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* gnu/packages/bioinformatics.scm (python-iced): New variable.
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* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
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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.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
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* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
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* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
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* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
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* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
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* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
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