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Author SHA1 Message Date
Ricardo Wurmus
7712154ccb
gnu: Add python-coolbox. 
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
e85b35070c
gnu: Add python-pybbi. 
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus
db13eb962f
gnu: Add python-strawc. 
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus
17c765e2e1
gnu: Add r-cytonorm. 
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus
f66759e0b2
gnu: Add ivar. 
* gnu/packages/bioinformatics.scm (ivar): New variable.
 2021-08-25 11:22:02 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
2ab5d08fbe
gnu: Add r-spectre. 
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
 2021-08-03 10:43:08 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
99ca1ae4f8
gnu: Add segemehl. 
* gnu/packages/bioinformatics.scm (segemehl): New variable.
 2021-07-26 11:08:13 +02:00
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
cc4906d13b
gnu: Add htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
 2021-07-22 10:50:58 +03:00
Efraim Flashner
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
Lars-Dominik Braun
73830b5da3
gnu: Add r-battenberg. 
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
ed636babfa
gnu: Add r-ascat. 
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
690df95d1a
gnu: Add nanosv. 
* gnu/packages/bioinformatics.scm (nanosv): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
2b665b8a49
gnu: Add python-pyvcf. 
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
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
Lars-Dominik Braun
18a02fe7ca
gnu: Add tombo. 
* gnu/packages/bioinformatics.scm (tombo): New variable.
 2021-07-21 13:36:07 +02:00
Julien Lepiller
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
Ludovic Courtès
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
Ludovic Courtès
b17ee44212
gnu: Do not import (gnu packages commencement). 
Line introduced in 4efbf56e53.

* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
 2021-07-01 17:13:13 +02:00
Efraim Flashner
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
Ricardo Wurmus
44bccf414b
gnu: Add perl-cworld-dekker. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
 2021-06-22 08:40:56 +02:00
Ricardo Wurmus
8a62d8685a
gnu: Add python-iced. 
* gnu/packages/bioinformatics.scm (python-iced): New variable.
 2021-06-21 13:02:39 +02:00
Ricardo Wurmus
748d3a2b8a
gnu: Add python-cgatcore. 
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
 2021-06-14 23:13:56 +02:00
Maxim Cournoyer
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
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
Efraim Flashner
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
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
Efraim Flashner
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
Mădălin Ionel Patrașcu
d1e7b50dbf
gnu: python-cooler: Update to 0.8.11. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
 2021-06-06 08:33:21 +02:00
Ricardo Wurmus
f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
 2021-06-05 09:12:39 +02:00
Roel Janssen
7382aa00b8
gnu: python-scanpy: Update to 1.7.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
 2021-06-04 23:51:35 +02:00
Ricardo Wurmus
d06ae05808
gnu: Add pigx-sars-cov2-ww. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
 2021-06-04 12:57:08 +02:00
Ricardo Wurmus
0928e55266
gnu: Add fit-sne. 
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
 2021-06-03 12:22:29 +02:00