c82b723bf8
gnu: Add megadepth.
...
* gnu/packages/bioinformatics.scm (megadepth): New variable.
2021-09-06 14:48:24 +02:00
c75b30d58f
gnu: Add r-catch.
...
* gnu/packages/bioinformatics.scm (r-catch): New variable.
2021-09-01 14:53:36 +02:00
4abf226833
gnu: Add scregseg.
...
* gnu/packages/bioinformatics.scm (scregseg): New variable.
2021-08-31 23:11:06 +02:00
a1ee212184
gnu: python-strawc: Propagate pybind11.
...
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
2021-08-31 23:11:05 +02:00
55cb5a62a1
gnu: python-scanpy: Propagate sinfo.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
2021-08-31 23:11:05 +02:00
7712154ccb
gnu: Add python-coolbox.
...
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
2021-08-30 18:29:57 +02:00
b105655670
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.
2021-08-30 18:29:57 +02:00
d84ead8174
gnu: Add python-dna-features-viewer.
...
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
2021-08-30 18:29:56 +02:00
e85b35070c
gnu: Add python-pybbi.
...
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
2021-08-30 18:29:56 +02:00
db13eb962f
gnu: Add python-strawc.
...
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
2021-08-27 13:37:29 +02:00
17c765e2e1
gnu: Add r-cytonorm.
...
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
2021-08-27 13:37:29 +02:00
f66759e0b2
gnu: Add ivar.
...
* gnu/packages/bioinformatics.scm (ivar): New variable.
2021-08-25 11:22:02 +02:00
27952318a5
gnu: fastp: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
2021-08-20 10:49:48 +02:00
a79ad5fce5
gnu: pigx-rnaseq: Update to 0.0.19.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
2021-08-13 15:23:39 +02:00
907f835e19
gnu: pigx-rnaseq: Update to 0.0.18.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
2021-08-11 19:33:38 +02:00
f1b64c435a
gnu: pigx-sars-cov2-ww: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
2021-08-05 16:46:34 +02:00
2ab5d08fbe
gnu: Add r-spectre.
...
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
2021-08-03 10:43:08 +02:00
3e5eff8c30
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.
2021-07-26 11:54:21 +02:00
99ca1ae4f8
gnu: Add segemehl.
...
* gnu/packages/bioinformatics.scm (segemehl): New variable.
2021-07-26 11:08:13 +02:00
fd8aea010f
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.
2021-07-22 10:58:22 +03:00
877792a6a7
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.
2021-07-22 10:57:41 +03:00
cc4906d13b
gnu: Add htslib-1.10.
...
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22 10:50:58 +03:00
309b38bed6
gnu: python-biopython: Update to 1.73.
...
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
2021-07-22 09:14:12 +03:00
73830b5da3
gnu: Add r-battenberg.
...
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21 13:36:08 +02:00
ed636babfa
gnu: Add r-ascat.
...
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
2021-07-21 13:36:08 +02:00
690df95d1a
gnu: Add nanosv.
...
* gnu/packages/bioinformatics.scm (nanosv): New variable.
2021-07-21 13:36:08 +02:00
2b665b8a49
gnu: Add python-pyvcf.
...
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
2021-07-21 13:36:08 +02:00
086c6800cf
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.
2021-07-21 13:36:08 +02:00
18a02fe7ca
gnu: Add tombo.
...
* gnu/packages/bioinformatics.scm (tombo): New variable.
2021-07-21 13:36:07 +02:00
ef79d6c5d6
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.
2021-07-05 16:54:11 +02:00
ebb8e44a4a
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'.
2021-07-01 17:13:13 +02:00
b17ee44212
gnu: Do not import (gnu packages commencement).
...
Line introduced in 4efbf56e53
2021-07-01 17:13:13 +02:00
07d2c72d39
gnu: ensembl-vep: Use a source file-name.
...
* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
2021-06-22 13:49:05 +03:00
44bccf414b
gnu: Add perl-cworld-dekker.
...
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
2021-06-22 08:40:56 +02:00
8a62d8685a
gnu: Add python-iced.
...
* gnu/packages/bioinformatics.scm (python-iced): New variable.
2021-06-21 13:02:39 +02:00
748d3a2b8a
gnu: Add python-cgatcore.
...
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
2021-06-14 23:13:56 +02:00
ea0a51071e
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.
2021-06-14 00:24:42 -04:00
ac51eb1125
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.
2021-06-08 22:43:47 +02:00
c9e8e7b0bf
gnu: pigx-bsseq: Update to 0.1.5.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
2021-06-08 16:35:17 +02:00
dd3698c1ac
gnu: python-hicmatrix: Update to 15.
...
* 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>
2021-06-08 16:35:17 +02:00
61bce4d143
gnu: python-mappy: Move to (gnu packages bioinformatics).
...
* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
2021-06-08 09:50:55 +03:00
4a01e00a13
gnu: pigx-rnaseq: Update to 0.0.17.
...
* 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.
2021-06-08 00:53:06 +02:00
be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
2021-06-07 16:50:33 +02:00
bb38287570
gnu: salmon: Update to 1.4.0.
...
* 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.
2021-06-07 16:50:33 +02:00
9875dae429
gnu: macs: Update to 2.2.7.1.
...
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
2021-06-07 16:50:33 +02:00
1ace395f9c
gnu: libgff: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
2021-06-07 16:50:33 +02:00
176513f5f3
gnu: jellyfish: Update to 2.3.0.
...
* 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.
2021-06-07 16:50:33 +02:00
1ac8f05103
gnu: multiqc: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
2021-06-07 10:53:16 +02:00
a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3.
...
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-06-07 10:38:54 +03:00
b65c02e2d3
gnu: freebayes: Update to 1.3.5.
...
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-06-06 12:13:28 +03:00
Ricardo Wurmus
Efraim Flashner
Lars-Dominik Braun
Julien Lepiller
Ludovic Courtès
Maxim Cournoyer
Mădălin Ionel Patrașcu