de48bcee07
gnu: Add r-gg3d.
...
* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
2023-01-09 14:50:26 +01:00
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
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
edbacab995
gnu: Use old setuptools in packages that relies on use_2to3 conversion.
...
This fixes a regression since 520cdf8058
2023-01-07 21:04:26 +01:00
1dd8359fa2
gnu: bbmap: Update to 39.01.
...
* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
2023-01-06 15:12:07 +01:00
f72dc615ab
gnu: bbmap: Use gexp.
...
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
2023-01-06 15:11:48 +01:00
04ea0e7de4
gnu: nanopolish: Drop input labels.
...
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
2023-01-06 15:01:05 +01:00
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
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
067c8a7445
gnu: filtlong: Use gexp.
...
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
2023-01-06 14:05:58 +01:00
0070e52ade
gnu: filtlong: Drop input labels.
...
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
2023-01-06 13:59:04 +01:00
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
e20ca244db
gnu: ngless: Use gexp.
...
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
2023-01-06 13:56:34 +01:00
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
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
10e1025c63
gnu: Add scallop.
...
* gnu/packages/bioinformatics.scm (scallop): New variable.
2023-01-04 17:14:01 +01:00
cad1789b3e
gnu: Add python-bcbio-gff.
...
* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
2023-01-03 15:43:25 +01:00
e84f17ea93
gnu: Add r-domultibarheatmap.
...
* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
2022-12-30 15:06:12 +01:00
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
d8a9d55b57
gnu: Add r-bedtorch.
...
* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
2022-12-22 11:18:02 +01:00
6d2f312b23
gnu: Add r-rhtslib12.
...
* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable.
2022-12-22 11:17:52 +01:00
2a4930a1e6
gnu: Add wiggletools.
...
* gnu/packages/bioinformatics.scm (wiggletools): New variable.
2022-12-22 10:29:20 +01:00
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
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
9e495087d2
gnu: Add vembrane.
...
* gnu/packages/bioinformatics.scm (vembrane): New variable.
2022-12-21 23:12:41 +01:00
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
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
50948b8c3d
gnu: htslib: Update to 1.16.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.16.
2022-12-21 23:12:40 +01:00
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
5ccc017389
gnu: Add htslib-1.14.
...
* gnu/packages/bioinformatics.scm (htslib-1.14): New variable.
2022-12-21 23:12:40 +01:00
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
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
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
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
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
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
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
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
eaf5198a5e
gnu: pbbam: Drop input labels.
...
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
2022-12-13 16:31:55 +01:00
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
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
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
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
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
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
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
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
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
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
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
Antero Mejr
Marius Bakke
Navid Afkhami