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* 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.
* gnu: python-scanpy: Propagate sinfo.Ricardo Wurmus2021-08-31
| | | | | | * gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move python-sinfo from here... [propagated-inputs]: ...to here.
* gnu: Add python-coolbox.Ricardo Wurmus2021-08-30
| | | | * gnu/packages/bioinformatics.scm (python-coolbox): New variable.
* gnu: python-scanpy: Update to 1.8.1.Ricardo Wurmus2021-08-30
| | | | | | * 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.
* gnu: Add python-dna-features-viewer.Ricardo Wurmus2021-08-30
| | | | * gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
* gnu: Add python-pybbi.Ricardo Wurmus2021-08-30
| | | | * gnu/packages/bioinformatics.scm (python-pybbi): New variable.
* gnu: Add python-strawc.Ricardo Wurmus2021-08-27
| | | | * gnu/packages/bioinformatics.scm (python-strawc): New variable.
* gnu: Add r-cytonorm.Ricardo Wurmus2021-08-27
| | | | * gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
* gnu: Add ivar.Ricardo Wurmus2021-08-25
| | | | * gnu/packages/bioinformatics.scm (ivar): New variable.
* gnu: fastp: Update to 0.20.1.Ricardo Wurmus2021-08-20
| | | | | * gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1. [arguments]: Set PREFIX instead of BINDIR.
* gnu: pigx-rnaseq: Update to 0.0.19.Ricardo Wurmus2021-08-13
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
* gnu: pigx-rnaseq: Update to 0.0.18.Ricardo Wurmus2021-08-11
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
* gnu: pigx-sars-cov2-ww: Update to 0.0.3.Ricardo Wurmus2021-08-05
| | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
* gnu: Add r-spectre.Ricardo Wurmus2021-08-03
| | | | * gnu/packages/bioinformatics.scm (r-spectre): New variable.
* gnu: Add seqan 3.Ricardo Wurmus2021-07-26
| | | | | | | * 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.
* gnu: Add segemehl.Ricardo Wurmus2021-07-26
| | | | * gnu/packages/bioinformatics.scm (segemehl): New variable.
* gnu: python-pysam: Make the check phase honor the tests? argument.Efraim Flashner2021-07-22
| | | | | * gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f.
* gnu: python-pysam: Update to 0.16.0.1.Efraim Flashner2021-07-22
| | | | | | | | | | | | * 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.
* gnu: Add htslib-1.10.Efraim Flashner2021-07-22
| | | | * gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
* gnu: python-biopython: Update to 1.73.Efraim Flashner2021-07-22
| | | | * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
* gnu: Add r-battenberg.Lars-Dominik Braun2021-07-21
| | | | * gnu/packages/bioinformatics.scm (r-battenberg): New variable.
* gnu: Add r-ascat.Lars-Dominik Braun2021-07-21
| | | | * gnu/packages/bioinformatics.scm (r-ascat): New variable.
* gnu: Add nanosv.Lars-Dominik Braun2021-07-21
| | | | * gnu/packages/bioinformatics.scm (nanosv): New variable.
* gnu: Add python-pyvcf.Lars-Dominik Braun2021-07-21
| | | | * gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
* gnu: checkm: Rename and update to 1.1.3.Lars-Dominik Braun2021-07-21
| | | | | | | | | | | 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.
* gnu: Add tombo.Lars-Dominik Braun2021-07-21
| | | | * gnu/packages/bioinformatics.scm (tombo): New variable.
* gnu: Add ocaml-sqlite3.Julien Lepiller2021-07-05
| | | | | | | * 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.
* gnu: bioperl-minimal: Avoid top-level cross-module references.Ludovic Courtès2021-07-01
| | | | | | | | 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'.
* gnu: Do not import (gnu packages commencement).Ludovic Courtès2021-07-01
| | | | | | | Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64. * gnu/packages/bioinformatics.scm: Remove unused (gnu packages commencement) import.
* gnu: ensembl-vep: Use a source file-name.Efraim Flashner2021-06-22
| | | | | * gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name field.
* gnu: Add perl-cworld-dekker.Ricardo Wurmus2021-06-22
| | | | * gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
* gnu: Add python-iced.Ricardo Wurmus2021-06-21
| | | | * gnu/packages/bioinformatics.scm (python-iced): New variable.
* gnu: Add python-cgatcore.Ricardo Wurmus2021-06-14
| | | | * gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
* gnu: Rename qtbase to qtbase-5.Maxim Cournoyer2021-06-14
| | | | | | | | | | | | 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.
* gnu: pigx-sars-cov2-ww: Update to 0.0.2.Ricardo Wurmus2021-06-08
| | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2. [inputs]: Add wget.
* gnu: pigx-bsseq: Update to 0.1.5.Ricardo Wurmus2021-06-08
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
* gnu: python-hicmatrix: Update to 15.Mădălin Ionel Patrașcu2021-06-08
| | | | | | | | * 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>
* gnu: python-mappy: Move to (gnu packages bioinformatics).Efraim Flashner2021-06-08
| | | | | * gnu/packages/python-xyz.scm (python-mappy): Move to ... * gnu/packages/bioinformatics.scm: ... here.
* gnu: pigx-rnaseq: Update to 0.0.17.Ricardo Wurmus2021-06-08
| | | | | | | | * 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.
* gnu: pigx-rnaseq: Adjust to upgrade of salmon.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase "use-latest-salmon".
* gnu: salmon: Update to 1.4.0.Ricardo Wurmus2021-06-07
| | | | | | | | | * 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.
* gnu: macs: Update to 2.2.7.1.Ricardo Wurmus2021-06-07
| | | | * gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
* gnu: libgff: Update to 2.0.0.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0. [home-page]: Update to new home.
* gnu: jellyfish: Update to 2.3.0.Ricardo Wurmus2021-06-07
| | | | | | | * 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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