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3563 Commits

Author SHA1 Message Date
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
Maxim Cournoyer
990a4822f1
Merge branch 'staging' into core-updates 
Conflicts resolved in:
	gnu/local.mk
	gnu/packages/cran.scm
	gnu/packages/gnome.scm
	gnu/packages/gtk.scm
	gnu/packages/icu4c.scm
	gnu/packages/java.scm
	gnu/packages/machine-learning.scm
	gnu/packages/tex.scm
 2022-09-27 15:59:30 -04:00
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
Ricardo Wurmus
cd5bbb9b42
gnu: python-cooler: Do not use flake8. 
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add build phase
'do-not-use-flake8.
 2022-09-21 22:19:33 +02:00
Ricardo Wurmus
d871080a41
gnu: Add r-chromunity. 
* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
a7f6392caa
gnu: Add r-skitools. 
* gnu/packages/bioinformatics.scm (r-skitools): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
af663c9e48
gnu: Add r-gchain. 
* gnu/packages/bioinformatics.scm (r-gchain): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
6ad4d74aca
gnu: Add r-gtrack. 
* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
29634a4ce3
gnu: Add r-bamutils. 
* gnu/packages/bioinformatics.scm (r-bamutils): New variable.
 2022-09-21 11:09:45 +02:00
Ricardo Wurmus
4bd64dde2b
gnu: Add r-gutils. 
* gnu/packages/bioinformatics.scm (r-gutils): New variable.
 2022-09-21 11:09:41 +02:00
Ricardo Wurmus
8084e3bdb3
gnu: python-pyvcf: Update to 0.6.8-0.476169c. 
* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
 2022-09-20 17:02:34 +02:00
Ricardo Wurmus
9ed635cd9a
gnu: python-pyvcf: Use older setuptools. 
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Replace
python-setuptools with python-setuptools-for-tensorflow.
 2022-09-20 17:02:34 +02:00
Marius Bakke
a91cf65a7e
gnu: Python: Update to 3.10.7. 
* gnu/packages/python.scm (python-3.9): Rename to ...
(python-3.10): ... this.  Update to 3.10.7.
[source](patches): Remove 'python-3-no-static-libs.patch' in favor of ...
[arguments]: Add #:configure-flags.
(python-3): Refer to PYTHON-3.10.
* gnu/packages/patches/python-3-fix-tests.patch: Refresh.
* gnu/packages/patches/python-3-no-static-lib.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/version-control.scm (mercurial)[native-search-paths]: Adjust
Python version.
* gnu/packages/admin.scm (ansible)[native-search-paths]: Likewise.
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Replace hard-coded
python3.9 paths with python3.10.
* gnu/packages/cran.scm (r-torch)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (liblantern)[arguments]: Likewise.
 2022-09-18 17:06:05 +02:00
Marius Bakke
7e0f2728a4
Merge branch 'staging' into core-updates 2022-09-16 19:11:43 +02:00
Maxim Cournoyer
b736af1824
gnu: catch-framework2: Rename variable to catch2. 
Automated with:

    git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i
 2022-09-15 20:15:56 -04:00
Maxim Cournoyer
4920f6e634
Merge branch 'staging' into core-updates 
Conflicts resolved in:
	gnu/local.mk
	gnu/packages/cmake.scm
	gnu/packages/glib.scm
	gnu/packages/gnome.scm
	gnu/packages/gtk.scm
	gnu/packages/sdl.scm

pango-next, vala-next and librsvg-bootstrap were removed in the process.
 2022-09-15 11:43:21 -04:00
Ricardo Wurmus
a7af25ad31
gnu: kraken2: Update to 2.1.2. 
* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2.
 2022-09-13 17:35:38 +02:00
Marius Bakke
1d526f5035
Merge branch 'staging' into core-updates 2022-09-10 17:30:17 +02:00
Christopher Baines
ad1d3f98b1
gnu: Add comments to the bottom of a few package modules. 
This will hopefully discourage patches which add new packages to the bottom of
files, as this increases the likelihood of conflicts when applying patches.

If there are more specific ways that packages should be arranged in specific
modules, this message can be updated accordingly.

* gnu/packages/bioconductor.scm: Add comment discouraging adding packages to
the bottom of the file.
* gnu/packages/bioinformatics.scm: ditto.
* gnu/packages/cran.scm: ditto.
* gnu/packages/crates-io.scm: ditto.
* gnu/packages/emacs-xyz.scm: ditto.
* gnu/packages/golang.scm: ditto.
* gnu/packages/guile-xyz.scm: ditto.
* gnu/packages/haskell-xyz.scm: ditto.
* gnu/packages/java.scm: ditto.
* gnu/packages/julia-xyz.scm: ditto.
* gnu/packages/lisp-xyz.scm: ditto.
* gnu/packages/ocaml.scm: ditto.
* gnu/packages/perl.scm: ditto.
* gnu/packages/python-science.scm: ditto.
* gnu/packages/python-xyz.scm: ditto.
* gnu/packages/ruby.scm: ditto.
* gnu/packages/tex.scm: ditto.
 2022-09-10 10:45:27 +01:00
Marius Bakke
884548b476
Merge branch 'staging' into core-updates 2022-09-08 21:12:52 +02:00
Marius Bakke
453e7dd8c4
gnu: tombo: Disable tests. 
* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
 2022-09-07 17:36:42 +02:00
Marius Bakke
58863b93b0
Merge branch 'staging' into core-updates 2022-09-01 23:26:57 +02:00
Ricardo Wurmus
36445e4d96
gnu: pigx-bsseq: Update to 0.1.8. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.8.
 2022-08-31 09:12:03 +02:00
Mădălin Ionel Patrașcu
8c5246677c
gnu: r-dyngen: Update to 1.0.4. 
* gnu/packages/bioinformatics.scm (r-dyngnen): Update to 1.0.4.
[source]: Change to cran-uri source.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-30 23:01:58 +02:00
Marius Bakke
ad384816fe
Merge branch 'staging' into core-updates 2022-08-27 17:10:55 +02:00
Ricardo Wurmus
d26b29d263
gnu: Add flair. 
* gnu/packages/bioinformatics.scm (flair): New variable.
 2022-08-23 13:30:52 +02:00
Ricardo Wurmus
8d42898572
gnu: python-mappy: Update to 2.24. 
* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
 2022-08-23 13:29:17 +02:00
Ricardo Wurmus
f3a7d43281
gnu: Add r-kbet. 
* gnu/packages/bioinformatics.scm (r-kbet): New variable.
 2022-08-18 12:21:07 +02:00
Ricardo Wurmus
8aab1f7c73
gnu: Add go-github-com-biogo-biogo. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable.
 2022-08-16 16:52:15 +02:00
Ricardo Wurmus
2407416d0f
gnu: Add go-github-com-biogo-hts-fai. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable.
 2022-08-16 16:50:16 +02:00
Ricardo Wurmus
31e0ac6dcf
gnu: Add go-github-com-biogo-hts-csi. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable.
 2022-08-16 16:50:01 +02:00
Ricardo Wurmus
b4f389e1b9
gnu: Add go-github-com-biogo-hts-cram. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable.
 2022-08-16 16:44:58 +02:00
Ricardo Wurmus
e9bec5bd40
gnu: Add go-github-com-biogo-hts-bgzf. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable.
 2022-08-16 16:28:33 +02:00
Ricardo Wurmus
bb162a5103
gnu: Add go-github-com-biogo-hts-tabix. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable.
 2022-08-16 16:28:23 +02:00
Ricardo Wurmus
4645a5d3f6
gnu: Add go-github-com-biogo-hts-sam. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
 2022-08-16 16:28:11 +02:00
Ricardo Wurmus
b986325b13
gnu: Add go-github-com-biogo-hts-bam. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
 2022-08-16 16:23:04 +02:00
Ricardo Wurmus
2345cd49de
gnu: Add go-github-com-biogo-store-step. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
 2022-08-16 16:18:57 +02:00
Ricardo Wurmus
c42745ba39
gnu: Add go-github-com-biogo-store-llrb. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
 2022-08-16 16:18:48 +02:00
Ricardo Wurmus
5fae9e158d
gnu: Add go-github-com-biogo-store-kdtree. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
 2022-08-16 16:18:40 +02:00
Ricardo Wurmus
a33ee9bd51
gnu: Add go-github-com-biogo-store-interval. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
 2022-08-16 16:18:31 +02:00
Ricardo Wurmus
2b4dcc477b
gnu: Add go-github-com-biogo-graph. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
 2022-08-16 16:09:54 +02:00
Ricardo Wurmus
872e17ddc1
gnu: Add stpipeline. 
* gnu/packages/bioinformatics.scm (stpipeline): New variable.
 2022-08-16 15:22:07 +02:00
Ricardo Wurmus
9c2400c282
gnu: Add python-taggd. 
* gnu/packages/bioinformatics.scm (python-taggd): New variable.
 2022-08-16 15:22:07 +02:00
Ricardo Wurmus
752be79bf3
gnu: htseq: Update to 2.0.2. 
* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.2.
[source]: Fetch from git repository.
[arguments]: Delete 'build phase; run tests with pytest in 'check phase.
[propagated-inputs]: Add python-matplotlib and python-pysam.
[inputs]: Remove python-matplotlib and python-pysam.
[native-inputs]: Add python-pandas, python-pytest, python-scipy, and swig.
[synopsis]: Update.
[description]: Update.
 2022-08-16 15:22:06 +02:00
Ricardo Wurmus
c3c2dfdb5e
gnu: plink-ng: Build sources from 2.0 directory 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Disable tests; adjust
make flags; enter 2.0 directory in 'chdir phase; replace 'install phase.
[inputs]: Add zstd:lib.
 2022-08-15 18:08:20 +02:00
Marius Bakke
77eb3008e3
Merge branch 'staging' into core-updates 2022-08-11 23:36:10 +02:00
Ricardo Wurmus
26bdefd172
gnu: Add r-liana. 
* gnu/packages/bioinformatics.scm (r-liana): New variable.
 2022-08-10 15:44:28 +02:00
Ricardo Wurmus
fd4b8e9873
gnu: Add r-omnipathr/devel. 
* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
 2022-08-10 15:44:28 +02:00
Marius Bakke
0b55b036c1
gnu: cereal: Update to 1.3.2. 
* gnu/packages/serialization.scm (cereal): Update to 1.3.2.
[arguments]: Use G-expression.
(cereal-1.3.0): New variable.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Change from CEREAL to
CEREAL-1.3.0.
* gnu/packages/engineering.scm (prusa-slicer)[inputs]: Likewise.
 2022-08-10 00:28:59 +02:00
Mădălin Ionel Patrașcu
ec6499aad2
gnu: Add phyml. 
* gnu/packages/bioinformatics.scm (phyml): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-08 12:38:41 +02:00
Ricardo Wurmus
03858a7908
gnu: Add python-scanorama. 
* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus
c69c2c1c4d
gnu: python-intervaltree: Update to 3.1.0. 
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus
f1b9ae8c20
gnu: python-bbknn: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1.
[propagated-inputs]: Add python-pandas.
 2022-08-01 17:46:21 +02:00
Mădălin Ionel Patrașcu
8d7a721400
gnu: Add r-millefy. 
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
 2022-08-01 15:14:47 +02:00
Ricardo Wurmus
dc3ad40c6b
gnu: python-bbknn: Set NUMBA_CACHE_DIR. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'set-numba-cache-dir.
 2022-08-01 12:46:19 +02:00
Maxim Cournoyer
1ef04fb228
gnu: qtsvg: Rename variable to qtsvg-5. 
This is in preparation of the qtsvg update to version 6.

This change was automated via the following command:

  git grep -l '\bqtsvg\b' | xargs sed 's/qtsvg/qtsvg-5/g' -i
 2022-07-31 21:55:43 -04:00
Efraim Flashner
e6bdd94c38
gnu: plink-ng: Fix building on other architectures. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to add simde includes to CFLAGS.
[native-inputs]: Add simde.
 2022-07-28 23:47:40 +03:00
Efraim Flashner
99d1122f8b
gnu: plink-ng: Update to 2.00a3.3. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
 2022-07-28 22:55:07 +03:00
Marius Bakke
9044b086dd
Merge branch 'staging' into core-updates 2022-07-22 01:09:14 +02:00
Ricardo Wurmus
d84bedd830
gnu: Add python-cellbender. 
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
 2022-07-09 10:37:22 +02:00
Ricardo Wurmus
6211ecfec8
gnu: Add hh-suite. 
* gnu/packages/bioinformatics.scm (hh-suite): New variable.
 2022-07-06 14:00:21 +02:00
Ricardo Wurmus
a0125732ef
gnu: Add r-sccustomize. 
* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
 2022-07-04 13:48:58 +02:00
Thiago Jung Bauermann
4d77072c56
gnu: libsbml: Use regular check. 
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14
with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-07-02 11:28:28 +02:00
Ricardo Wurmus
81cf674a5d
gnu: Add python-ikarus. 
* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
 2022-07-01 14:54:26 +02:00
Ludovic Courtès
8655a71445
Merge branch master into core-updates 2022-06-22 18:48:00 +02:00
Ricardo Wurmus
f700223c3b
gnu: Add pyscenic. 
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
 2022-06-16 15:20:59 +02:00
Ricardo Wurmus
3535d8dc5a
gnu: Add python-arboreto. 
* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
 2022-06-16 15:20:59 +02:00
Ricardo Wurmus
fbe5707b73
gnu: Add python-ctxcore. 
* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
 2022-06-16 15:20:59 +02:00
Ludovic Courtès
8c3e9da13a
Merge branch 'master' into core-updates 2022-06-08 14:46:24 +02:00
Vagrant Cascadian
964cdd57fa
gnu: discrover: Use reproducible timestamps. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add
  'set-force-source-date phase.
 2022-06-06 15:08:18 -07:00
Vagrant Cascadian
b483ef1a88
gnu: python-pybedtools: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0.
  [description]: Update to satisfy guix lint.
  [license]: Update to expat and lgpl2.1+.
 2022-06-09 23:10:15 -07:00
Ricardo Wurmus
b540e5e6bb
gnu: pigx-scrnaseq: Update to 1.1.9. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
 2022-06-01 12:57:22 +02:00
Ricardo Wurmus
93c97bfffb
gnu: pigx-bsseq: Update to 0.1.7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove automake and autoconf.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2022-06-01 12:41:59 +02:00
Ricardo Wurmus
6e54ce9ca9
gnu: pigx-chipseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2022-06-01 12:19:48 +02:00
Ricardo Wurmus
cd95d7ddd1
gnu: pigx-rnaseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
 2022-06-01 11:07:27 +02:00
Ricardo Wurmus
0aae2f7f01
gnu: pigx-rnaseq: Update to 0.0.21. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
 2022-06-01 10:46:00 +02:00
Ricardo Wurmus
0c26c8da9d
gnu: pigx-rnaseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
 2022-06-01 10:46:00 +02:00
Ricardo Wurmus
b279e778ab
gnu: Add sylamer. 
* gnu/packages/bioinformatics.scm (sylamer): New variable.
 2022-06-01 00:17:05 +02:00
Maxim Cournoyer
c35e508b4a
gnu: Remove python2-biopython. 
* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer
ad030a0b7d
gnu: Remove pplacer-scripts. 
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer
d397cb6207
gnu: Remove pplacer. 
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer
026fca8b5b
gnu: Remove python2-checkm-genome. 
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
 2022-05-31 14:54:15 -04:00
Maxim Cournoyer
4d7bb37981
gnu: Remove fraggenescan. 
* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
 2022-05-31 14:54:02 -04:00
Maxim Cournoyer
6792b0b6cd
gnu: Remove python2-pysam. 
* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
 2022-05-31 14:53:35 -04:00
Maxim Cournoyer
955e7d628d
gnu: Remove find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
 2022-05-31 14:53:34 -04:00
Maxim Cournoyer
a5e29cd838
gnu: Remove gess. 
* gnu/packages/bioinformatics.scm (gess): Delete variable.
 2022-05-31 14:53:34 -04:00
Maxim Cournoyer
c30ab2c0b4
gnu: Remove pyicoteo. 
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer
ba09192168
gnu: Remove python2-pbcore. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer
8287979669
gnu: Remove python2-pyfaidx. 
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
850bd0c329
gnu: Remove python2-screed. 
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
a94bc7798a
gnu: Remove miso. 
* gnu/packages/bioinformatics.scm (miso): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
23e133a907
gnu: Remove python2-warpedlmm. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bb35b50adc
gnu: Remove poretools. 
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bcdd45be6f
gnu: Remove python2-dendropy. 
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
d2c971e67b
gnu: Remove bamm. 
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
1010c05800
gnu: Remove python2-pybedtools. 
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
725b562962
gnu: Remove python2-htseq. 
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
8bcb07d089
gnu: Remove pepr. 
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
3d63c5f1ba
gnu: tetoolkit: Update to 2.2.1b. 
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse.  Replace python2-pysam with python-pysam.
[home-page]: Update URL.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
d29d50a556
gnu: Remove python2-pybigwig. 
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
98c4f97d18
gnu: Remove ribodiff. 
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
9f4c958d62
gnu: Remove grit. 
* gnu/packages/bioinformatics.scm (grit): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
7963e12568
gnu: Remove python2-fastalite. 
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
 2022-05-31 14:52:16 -04:00
Ricardo Wurmus
0bcd28e58c
gnu: python-scanpy: Update to 1.9.1. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
 2022-05-30 23:09:46 +02:00
Ricardo Wurmus
cb115ba722
gnu: pigx-sars-cov-2: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
 2022-05-29 00:39:19 +02:00
Ricardo Wurmus
df3e5cfa05
gnu: pigx-bsseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
 2022-05-29 00:34:29 +02:00
Ricardo Wurmus
b64f4a1245
gnu: pigx-scrnaseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
 2022-05-29 00:29:19 +02:00
Ricardo Wurmus
add551f651
gnu: pigx-chipseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
 2022-05-29 00:18:48 +02:00
Tobias Geerinckx-Rice
b015a15c57
gnu: Fix all this damn packages. 
* gnu/packages/bioinformatics.scm (r-icellnet)[description]:
Fix ‘this packages’ typo.
* gnu/packages/cran.scm (r-add2ggplot)[description]: Likewise.
* gnu/packages/crates-io.scm (rust-const-oid-0.6, rust-pem-rfc7468-0.2)
(rust-scrypt-0.8)[description]: Likewise.
 2022-05-22 02:00:00 +02:00
Josselin Poiret
dab819d5c4
Move (gnu platform) and (gnu platforms ...) to guix/. 
* gnu/platform.scm:
* gnu/platforms/arm.scm:
* gnu/platforms/hurd.scm:
* gnu/platforms/mips.scm:
* gnu/platforms/powerpc.scm:
* gnu/platforms/riscv.scm:
* gnu/platforms/s390.scm:
* gnu/platforms/x86.scm: Move to guix/.

* Makefile.am:
* doc/guix.texi (Porting to a New Platform):
* etc/release-manifest.scm:
* gnu/ci.scm:
* gnu/image.scm:
* gnu/local.mk:
* gnu/packages/bioinformatics.scm:
* gnu/packages/bootstrap.scm:
* gnu/packages/cross-base.scm:
* gnu/packages/instrumentation.scm:
* gnu/packages/linux.scm:
* gnu/system/image.scm:
* gnu/system/images/hurd.scm:
* gnu/system/images/novena.scm:
* gnu/system/images/pine64.scm:
* gnu/system/images/pinebook-pro.scm:
* gnu/system/images/rock64.scm:
* guix/scripts/build.scm:
* guix/scripts/system.scm:
* guix/self.scm: Update (gnu platform...) to (guix platform...).

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-05-25 09:27:25 +02:00
Mathieu Othacehe
b55310603f
linux: Remove system->linux-architecture procedure. 
* gnu/packages/linux.scm (system->linux-architecture): Remove it.
(make-linux-libre-headers*, make-linux-libre*): Adapt them.
* guix/build-system/linux-module.scm (system->arch): Adapt it.
* gnu/packages/instrumentation.scm (uftrace): Ditto.
* gnu/packages/cross-base.scm (cross-kernel-headers): Ditto.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Ditto.
* doc/guix.texi (Porting to a new platform): Update it.
 2022-05-22 15:15:33 +02:00
Arun Isaac
a1a55e5b60
gnu: fastahack: Wrap long line. 
* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
 2022-05-12 12:59:18 +05:30