futurile/guix-play
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
110,266 Commits 3 Branches 0 Tags 412 MiB
643b859834
Commit Graph

3457 Commits

Author SHA1 Message Date
Navid Afkhami
43b7a033e3
gnu: Add r-tsis. 
* gnu/packages/bioinformatics.scm (r-tsis): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-01-20 11:06:43 +01:00
Navid Afkhami
ddfe68ebbe
gnu: Add r-doubletcollection. 
* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-01-20 11:02:37 +01:00
Simon Tournier
a7f1a1c0f0
gnu: Add python-vireosnp. 
* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
 2023-01-20 10:40:59 +01:00
Tobias Geerinckx-Rice
ae071e21f3
gnu: gdcm: Fix recursive Git source hash. 
The hash being used covered only the gdcm repository, not the gdcmdata
submodule.

* gnu/packages/bioinformatics.scm (gdcm)[source]: Update hash.

Reported by civodul in #guix.
 2023-01-15 01:00:00 +01:00
Tor-björn Claesson
2bdbd962e3
gnu: gdcm: Update to 3.0.20. 
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20.
[home-page, license]: Update.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-17 16:05:20 +01:00
Ricardo Wurmus
bdcdab3676
gnu: r-cytonorm: Update to 0.0.10-1.166f9ff. 
* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
 2023-01-16 23:54:20 +01:00
Ricardo Wurmus
9ad5c3deea
gnu: r-signac: Update to 1.9.0-1.af41427. 
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.9.0-1.af41427.
[propagated-inputs]: Remove r-ggforce, r-ggrepel, r-ggseqlogo, r-lsa,
r-qlcmatrix, and r-seurat; add r-vctrs.
 2023-01-13 10:51:23 +01:00
Marius Bakke
7f7907335d
gnu: python-cellbender: Update source hash. 
The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52
to d92cfc5a55c8b1771348468035993c52df975170.

* gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
 2023-01-13 03:19:40 +01:00
Simon Tournier
483bc044eb
gnu: Add cellsnp-lite. 
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
 2023-01-12 21:37:56 +01:00
Ricardo Wurmus
de48bcee07
gnu: Add r-gg3d. 
* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
 2023-01-09 14:50:26 +01:00
Ricardo Wurmus
a4d9ce5488
gnu: Move Java XML packages to new module. 
* gnu/packages/xml.scm (java-simple-xml, java-jaxp,
java-apache-xml-commons-resolver, java-jaxen, java-xom, java-xsdlib,
java-xpp3, java-xmlpull2, java-xmlpull-api-v1, java-dom4j, java-kxml2,
java-stax, java-jettison, java-jdom2, java-xstream, java-mxparser): Move these
variables from here...
* gnu/packages/java-xml.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register new file.
* gnu/packages/axoloti.scm,
gnu/packages/batik.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/groovy.scm,
gnu/packages/java.scm,
gnu/packages/maven.scm: Adjust module imports.
 2023-01-08 23:20:59 +01:00
Antero Mejr
15caeb745c
gnu: Add gdcm. 
* gnu/packages/bioinformatics.scm (gdcm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-08 16:11:45 +01:00
Marius Bakke
edbacab995
gnu: Use old setuptools in packages that relies on use_2to3 conversion. 
This fixes a regression since 520cdf8058 where
the use_2to3 functionality was removed from setuptools.

* gnu/packages/graph.scm (python-louvain)[native-inputs]: Change from
PYTHON-SETUPTOOLS to PYTHON-SETUPTOOLS-57.
* gnu/packages/python-check.scm (python-parameterizedtestcase)[native-inputs]:
Likewise.
* gnu/packages/python-xyz.scm (python-anyjson)[native-inputs]: Add
PYTHON-SETUPTOOLS-57.
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Change from
PYTHON-SETUPTOOLS-FOR-TENSORFLOW to PYTHON-SETUPTOOLS-57.
 2023-01-07 21:04:26 +01:00
Ricardo Wurmus
1dd8359fa2
gnu: bbmap: Update to 39.01. 
* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
 2023-01-06 15:12:07 +01:00
Ricardo Wurmus
f72dc615ab
gnu: bbmap: Use gexp. 
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
 2023-01-06 15:11:48 +01:00
Ricardo Wurmus
04ea0e7de4
gnu: nanopolish: Drop input labels. 
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
 2023-01-06 15:01:05 +01:00
Ricardo Wurmus
24e5dbb57a
gnu: nanopolish: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0.
[source]: Update snippet.
[arguments]: Use gexp; use cc-for-target; drop #T from build phases.
[inputs]: Add minimap2.
[native-inputs]: Add cmake-minimal.
 2023-01-06 14:51:55 +01:00
Ricardo Wurmus
8ace894681
gnu: filtlong: Use Python 3. 
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with
python-wrapper.
 2023-01-06 14:06:13 +01:00
Ricardo Wurmus
067c8a7445
gnu: filtlong: Use gexp. 
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
 2023-01-06 14:05:58 +01:00
Ricardo Wurmus
0070e52ade
gnu: filtlong: Drop input labels. 
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
 2023-01-06 13:59:04 +01:00
Ricardo Wurmus
f5ffcd31c2
gnu: filtlong: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
 2023-01-06 13:58:05 +01:00
Ricardo Wurmus
e20ca244db
gnu: ngless: Use gexp. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
 2023-01-06 13:56:34 +01:00
Ricardo Wurmus
648c370f33
gnu: ngless: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Remove trailing #T.
 2023-01-06 13:45:06 +01:00
Ricardo Wurmus
ec5b9fe27e
gnu: bamtools: Build shared libraries. 
* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared
libraries instead of static libs.
 2023-01-04 19:49:59 +01:00
Ricardo Wurmus
10e1025c63
gnu: Add scallop. 
* gnu/packages/bioinformatics.scm (scallop): New variable.
 2023-01-04 17:14:01 +01:00
Ricardo Wurmus
cad1789b3e
gnu: Add python-bcbio-gff. 
* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
 2023-01-03 15:43:25 +01:00
Ricardo Wurmus
e84f17ea93
gnu: Add r-domultibarheatmap. 
* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
 2022-12-30 15:06:12 +01:00
Ricardo Wurmus
bbada5967d
gnu: r-giotto: Update to 1.1.2-1.3c8067c. 
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c.
 2022-12-28 19:26:10 +01:00
Ricardo Wurmus
d8a9d55b57
gnu: Add r-bedtorch. 
* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
 2022-12-22 11:18:02 +01:00
Ricardo Wurmus
6d2f312b23
gnu: Add r-rhtslib12. 
* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable.
 2022-12-22 11:17:52 +01:00
Ricardo Wurmus
2a4930a1e6
gnu: Add wiggletools. 
* gnu/packages/bioinformatics.scm (wiggletools): New variable.
 2022-12-22 10:29:20 +01:00
Navid Afkhami
87c3fab854
gnu: Add python-episcanpy. 
* gnu/packages/bioinformatics.scm (python-episcanpy): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-12-22 00:17:43 +01:00
Navid Afkhami
d07543b886
gnu: Add python-bamnostic. 
* gnu/packages/bioinformatics.scm (python-bamnostic): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-12-22 00:14:05 +01:00
Ricardo Wurmus
9e495087d2
gnu: Add vembrane. 
* gnu/packages/bioinformatics.scm (vembrane): New variable.
 2022-12-21 23:12:41 +01:00
Ricardo Wurmus
1194cb1c40
gnu: python-plastid: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.0.
[source]: Fetch from git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests; add build phases 'unpack-test-data and
'build-extensions.
[inputs]: Add openssl.
[native-inputs]: Add test data.
 2022-12-21 23:12:40 +01:00
Ricardo Wurmus
bc4eac5d79
gnu: python-pysam: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.20.0.
[build-system]: Use pyproject-build-system.
 2022-12-21 23:12:40 +01:00
Ricardo Wurmus
50948b8c3d
gnu: htslib: Update to 1.16. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.16.
 2022-12-21 23:12:40 +01:00
Ricardo Wurmus
e34639c262
gnu: pbbam: Use htslib 1.14. 
* gnu/packages/bioinformatics.scm (pbbam)[propagated-inputs]: Replace htslib
with htslib-1.14.
 2022-12-21 23:12:40 +01:00
Ricardo Wurmus
5ccc017389
gnu: Add htslib-1.14. 
* gnu/packages/bioinformatics.scm (htslib-1.14): New variable.
 2022-12-21 23:12:40 +01:00
Ricardo Wurmus
9cb42f725a
gnu: python-scanpy: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'build and 'install phases; move pytest arguments
to #:test-flags; add 'pretend-version phase; replace custom 'check phase with
'delete-bad-tests phase.
 2022-12-18 15:46:18 +01:00
Ricardo Wurmus
6aebf864a7
gnu: python-multivelo: Simplify with pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'build and 'install phases.
 2022-12-18 15:46:18 +01:00
Ricardo Wurmus
1689215a30
gnu: bedtools-2.18: Use gexp. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp.
[native-inputs]: Drop package label.
 2022-12-14 22:47:43 +01:00
Ricardo Wurmus
3d2b2f12e5
gnu: bedops: Update to 2.4.41. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41.
[arguments]: Remove trailing #T from build phases; do not set BINDIR in
make-flags; set CC; replace 'install phase.
[native-inputs]: Add diffutils, perl, and which.
 2022-12-13 18:22:55 +01:00
Ricardo Wurmus
23322c2de8
gnu: tophat: Remove trailing #T from build phases and snippet. 
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from
snippet.
[arguments]: Remove trailing #T from build phases.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
b339e181e1
gnu: python-bx-python: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'build-extensions and 'disable-cython-doctests.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
de30c74b63
gnu: bioawk: Use gexp. 
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify
'install phase.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
057579495f
gnu: blasr-libcpp: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove
trailing #T from build phases.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
eaf5198a5e
gnu: pbbam: Drop input labels. 
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
8b2fdcb2c3
gnu: pbbam: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
684d046e6c
gnu: pbcopper: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus
53f65f7315
gnu: bedtools: Remove unnecessary quasiquotation. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote.
[native-inputs]: Drop input label.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
4f1a36bd7b
gnu: bamutils: Update to 1.0.15. 
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15.
[arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags.
[native-inputs]: Update libstatgen.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
8cc22866c2
gnu: bamtools: Update to 2.5.2. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2.
[arguments]: Enable tests; remove extra phases.
[inputs]: Add jsoncpp.
[native-inputs]: Add pkg-config.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
6d2afaf25b
gnu: aragorn: Update to 1.2.41. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41.
[source]: Fetch C source file from new location.
[arguments]: Drop trailing #T in build phases; use gexp.
[native-inputs]: Add origin for man page.
[home-page]: Update to new home page.
[license]: Update to GPLv3+.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus
e84042fdd4
gnu: cnvkit: Update to 0.9.9. 
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
1369b53d49
gnu: seqmagick: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
461dff2651
gnu: python-cgatcore: Update to 0.6.14. 
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
b72df3bbb3
gnu: python-dna-features-viewer: Update to 3.1.1. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus
b66b6bdf70
gnu: python-hicexplorer: Update to 3.7.2. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus
c3e330cf36
gnu: python-pygenometracks: Update to 3.5. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
6e9518e201
gnu: python-hicmatrix: Update to 16. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
5167881a60
gnu: python-biopython: Update to 1.80. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
2c8a53cb6b
gnu: bioperl-minimal: Remove trailing #T from build phase. 
* gnu/packages/bioinformatics.scm (bioperl-minimal)[arguments]: Remove
trailing #T from build phase.
 2022-12-12 14:37:03 +01:00
Ricardo Wurmus
fd44d489b5
gnu: python-biom-format: Update to 2.1.12. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12.
[arguments]: Remove "relax" phase; update "disable-broken-tests" phase.
[propagated-inputs]: Add python-scikit-bio.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus
b93e21a213
gnu: Add python-scikit-bio. 
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus
62da3f9837
gnu: python-pairtools: Update to 1.0.2. 
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2.
[source]: Update Github URL.
[arguments]: Update patch in "fix-references" phase.
[native-inputs]: Remove python-nose.
[inputs]: Remove.
[propagated-inputs]: Add python-bioframe, python-pandas, python-pysam,
python-pyyaml, and python-scipy.
[home-page]: Update.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus
089b2e4f65
gnu: python-pairtools: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests
conditionally.
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus
631ea9a411
gnu: python-pybedtools: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use
pyproject-build-system.
[arguments]: Import (guix build pyproject-build-system).
 2022-12-02 21:46:36 +01:00
Ricardo Wurmus
a268b1ba91
gnu: python-htsget: Update to 0.2.6. 
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6.
[build-system]: Use pyproject-build-system.
 2022-12-02 21:46:35 +01:00
Ricardo Wurmus
16ecce39d2
gnu: python-cellbender: Update to 0.2.2. 
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2.
[build-system]: Use pyproject-build-system.
 2022-12-02 21:46:35 +01:00
Ricardo Wurmus
62ddd3bc80
gnu: Add python-fanc. 
* gnu/packages/bioinformatics.scm (python-fanc): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2022-12-02 17:43:20 +01:00
Ricardo Wurmus
ee069ec651
gnu: Add python-genomic-regions. 
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2022-12-02 17:20:54 +01:00
Navid Afkhami
b095dac8e0
gnu: Add r-btools. 
* gnu/packages/bioinformatics.scm (r-btools): New variable.
 2022-11-25 11:17:56 +01:00
Ricardo Wurmus
ebde19092f
gnu: r-circus: Update to 0.1.7. 
* gnu/packages/bioinformatics.scm (r-circus): Update to 0.1.7.
[properties]: Add upstream-name property.
[propagated-inputs]: Add r-biocgenerics, r-genomeinfodb, and r-rtracklayer.
 2022-11-17 15:00:49 +01:00
Ricardo Wurmus
02db3f51b7
gnu: Add r-disgenet2r. 
* gnu/packages/bioinformatics.scm (r-disgenet2r): New variable.
 2022-11-15 11:03:24 +01:00
Mădălin Ionel Patrașcu
b4e3e02fd1
gnu: Add r-pando. 
* gnu/packages/bioinformatics.scm (r-pando): New variable.
 2022-11-09 09:55:14 +01:00
Mădălin Ionel Patrașcu
49e1a3a04b
gnu: Add python-cooltools. 
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
 2022-11-04 13:50:20 +01:00
Mădălin Ionel Patrașcu
14cbaac69c
gnu: Add python-bioframe. 
X-Debbugs-Cc: rekado@elephly.net

* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
 2022-11-04 13:39:12 +01:00
Ricardo Wurmus
1b0fea29a0
gnu: r-dyngen: Update to 1.0.5. 
* gnu/packages/bioinformatics.scm (r-dyngen): Update to 1.0.5.
 2022-11-04 10:01:05 +01:00
Vagrant Cascadian
15ff5eebb6
gnu: Fix various lint issues in synopsis and descriptions. 
* gnu/packages/android.scm (etc1tool)[synopsis]: Drop trailing period.
* gnu/packages/bioinformatics.scm (mudskipper)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-async-log-attributes-1)[synopsis]: Likewise.
  (rust-atomic-polyfill-1)[synopsis]: Likewise.
  (rust-modifier-0.1)[synopsis]: Likewise.
  (rust-openssl-macros-0.1)[synopsis]: Likewise.
  (rust-syn-mid-0.5)[synopsis]: Likewise.
  (rust-toml-edit-0.14)[synopsis]: Likewise.
  (rust-valuable-derive-0.1)[synopsis]: Likewise.
  (rust-inflections-1)[synopsis]: Likewise.
* gnu/packages/databases.scm (python-databases)[synopsis]: Likewise.
* gnu/packages/games.scm (liquidwar6)[synopsis]: Likewise.
* gnu/packages/golang.scm (go-golang.org-x-sync-errgroup)[synopsis]: Likewise.
* gnu/packages/guile-xyz.scm (guile-config)[synopsis]: Likewise.
* gnu/packages/haskell-web.scm (ghc-hxt-xpath)[synopsis]: Likewise.
* gnu/packages/haskell-xyz.scm (ghc-string-qq)[synopsis]: Likewise.
* gnu/packages/machine-learning.scm (python-lap)[synopsis]: Likewise.
  (python-pyro-api)[synopsis]: Likewise.
* gnu/packages/messaging.scm (python-librecaptcha)[synopsis]: Likewise.
* gnu/packages/python-check.scm (python-pytest-cram)[synopsis]: Likewise.
* gnu/packages/python-web.scm (python-jschema-to-python)[synopsis]: Likewise.
  (python-sarif-om)[synopsis]: Likewise.
  (python-socksio)[synopsis]: Likewise.
  (python-msrest)[synopsis]: Likewise.
* gnu/packages/tor.scm (torsocks)[synopsis]: Likewise.
* gnu/packages/cran.scm (r-rlist)[synopsis]: Remove leading article.
* gnu/packages/crates-io.scm (rust-clippy-lints-0.0.153)[synopsis]: Likewise.
  (rust-simplelog-0.11)[synopsis]: Likewise.
* gnu/packages/samba.scm (wsdd)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-spki-0.4)[synopsis]: Remove trailing
  whitespace.
* gnu/packages/golang.scm (go-github-com-mattn-go-zglob)[description]: Remove
  leading whitespace.
* gnu/packages/haskell-check.scm (ghc-crypto-cipher-tests)[description]:
  Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-ctype)[synopsis]: Remove trailing
  whitespace.
* gnu/packages/mpi.scm (openmpi-thread-multiple)[description]: Remove leading
  whitespace.
* gnu/packages/node-xyz.scm (node-string-decoder)[synopsis]: Remove trailing
  whitespace.
 2022-10-31 18:13:48 -07:00
Ricardo Wurmus
75b24abf09
gnu: flair: Update to 1.6.4. 
* gnu/packages/bioinformatics.scm (flair): Update to 1.6.4.
[propagated-inputs]: Add python-numpy and python-scipy.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
bb4f24b3ae
gnu: flair: Set R_HOME. 
* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
28950ed561
gnu: flair: Add missing R package. 
* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
 2022-10-28 15:00:20 +02:00
Ricardo Wurmus
176a501360
gnu: flair: Add missing R packages. 
* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2.
[inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman,
and r-rlang.
[arguments]: Add phase "wrap-executable".
 2022-10-27 18:21:22 +02:00
Mădălin Ionel Patrașcu
fe7b421d05
gnu: Add python-multivelo. 
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
 2022-10-27 15:15:19 +02:00
Hong.Li@mdc-berlin.de
358a1fdf7b
gnu: Add r-seuratwrappers. 
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
 2022-10-27 15:03:21 +02:00
Vagrant Cascadian
a2e4e3489b
gnu: Various typo fixes. 
* gnu/packages/emacs-xyz.scm (emacs-popup-kill-ring)[description]: Fix very
  sneaky "This packages" variant. Thanks to nckhexen!
* gnu/packages/bioinformatics.scm (r-icellnet)[description]: Fix use of
  "allows to".
* gnu/packages/check.scm (python-pytest-freezegun)[description]: Ditto.
* gnu/packages/linux.scm (tp-smapi-module)[description]: Ditto.
* gnu/packages/mail.scm (procmail): Ditto.
* gnu/packages/maths.scm (maxima): Ditto.
* gnu/packages/samba.scm (wsdd)[description]: Ditto.
* gnu/packages/ssh.scm (openssh): Ditto.
 2022-10-24 17:35:19 -07:00
Vagrant Cascadian
d3e982dccb
gnu: Fix typos. 
* gnu/packages/emacs-xyz.scm (emacs-piem)[description]: Fix use of "This
  packages".
* gnu/packages/tex.scm (texlive-hardwrap)[description]: Fix spelling of
  "arbitrary".
* gnu/packages/cran.scm (r-shinymanager)[description]: Fix spelling of
  "authentication".
* gnu/packages/lisp-xyz.scm (sbcl-utils-kt)[description]: Fix spelling of
  "developed".
* gnu/packages/crates-io.scm (rust-fs-utils-1)[description]: Fix spelling of
  "filesystem".
  [synopsis]: Likewise.
* gnu/packages/haxe.scm (neko)[description]: Fix spelling of "functions".
* gnu/packages/animation.scm (swftools)[description]: Fix needless
  pluralization of "information".
* gnu/packages/lisp-xyz.scm (sbcl-slot-extra-options)[description]: Fix
  spelling of "inheritance".
* gnu/packages/emacs-xyz.scm (emacs-js-comint)[description]: Fix spelling of
  "interpreter".
* gnu/packages/coq.scm (coq-mathcomp-finmap)[description]: Fix spelling of
  "library".
* gnu/services/lightdm.scm (lightdm-configuration): Fix spelling of
  "mechanism".
* gnu/packages/emacs-xyz.scm (emacs-citar-org-roam)[synopsis]: Fix spelling of
  "package".
* gnu/packages/games.scm (freerct)[description]: Fix spelling of
  "responsibilities".
* gnu/packages/statistics.scm (r-mixedpower)[description]: Fix spelling of
  "separate".
* gnu/packages/accessibility.scm (espeakup)[description]: Fix spelling of
  "speech".
* gnu/packages/bioinformatics.scm (r-skitools)[synopsis]: Fix spelling of
  "utilities".
* gnu/packages/golang.scm (go-github-com-savsgio-gotils)[synopsis]: Fix
  spelling of "utilities".
  [description]: Likewise.
* gnu/system.scm (boot-file-system-service os): Fix spelling of "utilities".
 2022-10-23 17:03:09 -07:00
Ricardo Wurmus
f24b66bf4a
gnu: pigx-sars-cov-2: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.8.
[arguments]: Add build phase 'unpack-databases; enable tests.
[native-inputs]: Add origins for databases; remove automake and autoconf.
[inputs]: Add r-data-table, r-deconvr, r-htmltools, r-jsonlite, r-knitr, and
r-mass.
 2022-10-08 12:06:41 +02:00
Christopher Baines
020dc0a1f1
gnu: plink: Change origin URL. 
pngu.mgh.harvard.edu seems to time out.

* gnu/packages/bioinformatics.scm (plink)[origin]. Change URL.
 2022-10-06 15:08:02 +01:00
Ricardo Wurmus
fd6cd9de86
gnu: Add megahit. 
* gnu/packages/bioinformatics.scm (megahit): New variable.
 2022-10-05 17:59:04 +02:00
Ricardo Wurmus
be1d561f1a
gnu: Add cd-hit-auxtools. 
* gnu/packages/bioinformatics.scm (cd-hit-auxtools): New variable.
 2022-10-05 14:28:24 +02:00
Ricardo Wurmus
3f627bf56b
gnu: cd-hit: Update to 4.8.1. 
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.8.1.
[arguments]: Do not use quasiquote; remove trailing #T from build phases.
[inputs]: Add zlib.
 2022-10-05 13:47:57 +02:00
Ricardo Wurmus
9ed65e6af7
gnu: kaiju: Update to 1.9.0. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0.
[arguments]: Use gexps; wrap scripts in install phase.
[inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip,
python-wrapper, tar, and wget.
 2022-10-04 23:10:56 +02:00
Ricardo Wurmus
1266b9ed11
gnu: salmon: Update to 1.9.0. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0.
[arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish
itlib headers.
[inputs]: Use new label-less list; move pufferfish origin from here...
[native-inputs]: ...to here.
 2022-09-30 22:43:21 +02:00
Ricardo Wurmus
729ce5fcf8
gnu: Add centrifuge. 
* gnu/packages/bioinformatics.scm (centrifuge): New variable.
 2022-09-30 16:59:18 +02:00
Ricardo Wurmus
1ee2d117d8
gnu: blast+: Build reproducibly. 
Fixes <https://issues.guix.gnu.org/42141>.

* gnu/packages/bioinformatics.scm (blast+)[source]: Do not record kernel
version and use fix set of random numbers.
 2022-09-29 23:21:16 +02:00
Ricardo Wurmus
c1716ab6ec
gnu: Add r-compgenomrdata. 
* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
 2022-09-26 17:21:57 +02:00
Ricardo Wurmus
cbe8391d7c
gnu: Add mudskipper. 
* gnu/packages/bioinformatics.scm (mudskipper): New variable.
 2022-09-23 00:21:40 +02:00
Ricardo Wurmus
1a1ff7ed8f
gnu: python-cooler: Skip broken test. 
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add another
patch for tests/test_util.py.
 2022-09-21 22:19:33 +02:00