2794caed7c
gnu: Add r-numbat.
...
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
2023-07-12 21:34:07 +02:00
3b524cde71
gnu: Add r-bpcells.
...
* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
2023-07-12 16:45:42 +02:00
de3b8684e9
gnu: r-pando: Fix hash.
...
* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash.
2023-07-06 23:29:05 +02:00
df5bf65f26
gnu: bismark: Update to 0.24.1.
...
* gnu/packages/bioinformatics.scm (bismark): Update to 0.24.1.
[source]: Delete bundled plot.ly.
[arguments]: Use plain list; remove trailing #T from build phases; adjust
'replace-plotly.js phase to account for use of script tags; adjust 'install
phase to install documentation in markdown format; add 'configure phase for
replacing references to tools.
[inputs]: Add bowtie, hisat2, minimap2, and samtools.
2023-07-06 23:29:05 +02:00
c66e5ef5f9
gnu: cutadapt: Update to 4.0.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable a single test; remove 'always-cythonize build phase; add
phase 'fix-test.
[native-inputs]: Add python-pytest-mock and python-pytest-timeout.
2023-07-03 16:37:45 +02:00
cb15c60d35
gnu: python-dnaio: Update to 0.10.0.
...
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.10.0.
[arguments]: Disable tests, because they don't exist.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools-scm; move python-xopen from here...
[propagated-inputs]: ...to here.
2023-07-03 16:36:53 +02:00
669f0eaed6
gnu: Add r-dtmm.
...
* gnu/packages/bioinformatics.scm (r-dtmm): New variable.
2023-07-03 13:42:47 +02:00
94ac93042f
gnu: Add rscape.
...
* gnu/packages/bioinformatics.scm (rscape): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-29 22:25:35 +02:00
10ff8ff4b5
gnu: r-pando: Update to 1.0.5.
...
* gnu/packages/bioinformatics.scm (r-pando): Update to 1.0.5.
[propagated-inputs]: Remove r-brms and r-xgboost; add r-grr and
r-matrixgenerics.
2023-06-29 12:01:22 +02:00
7f3c6d3b3b
gnu: sambamba: Fix building.
...
* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Remove
ld-gold-wrapper, bintutils-gold. Remove input labels.
2023-06-22 12:19:49 +03:00
7b535eb29b
gnu: bioruby: Update to 2.0.4.
...
* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4.
[arguments]: Update style.
2023-06-20 22:04:51 +01:00
74443c30f3
gnu: Add python-mudata.
...
* gnu/packages/bioinformatics.scm (python-mudata): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-09 17:09:38 +02:00
c348b1be38
gnu: Add python-mofax.
...
* gnu/packages/bioinformatics.scm (python-mofax): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-09 16:56:22 +02:00
f056d4f168
gnu: Add python-decoupler-py.
...
* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-06-06 21:35:37 +02:00
4f2ec0f2d1
gnu: python-bulkvis: Reference upstream issue.
...
* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment
with link to upstream issue for bokeh compatibility patch.
2023-06-05 17:20:52 +02:00
6559adea29
gnu: Add python-bulkvis.
...
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-05 17:11:15 +02:00
91e75bb35f
gnu: Add python-readpaf.
...
* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
2023-06-05 17:11:14 +02:00
c11b92a8aa
gnu: Add r-singlet.
...
* gnu/packages/bioinformatics.scm (r-singlet): New variable.
2023-06-02 21:18:26 +02:00
f09944461f
gnu: Add python-cell2cell.
...
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-02 19:54:27 +02:00
341b4b2a97
gnu: Add java-maxent.
...
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
2023-06-02 11:34:17 +02:00
d411b7d5e7
gnu: Add python-pyani.
...
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
2023-06-01 20:48:17 +02:00
525ef60ff4
gnu: Add python-illumina-utils.
...
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
2023-06-01 20:48:17 +02:00
ced6e0fe94
gnu: Add python-ete3.
...
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
2023-06-01 14:10:04 +02:00
60b71b0db4
gnu: Add python-gseapy.
...
* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
2023-05-26 14:36:14 +02:00
980d2cd73b
gnu: java-picard-1.113: Drop input package labels.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113)[inputs]: Drop labels.
2023-05-19 13:12:29 +02:00
1baf94dbbe
gnu: java-picard-1.113: Drop trailing #T from build phases.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Remove
trailing #T from build phases.
2023-05-19 13:12:29 +02:00
69d74e35b2
gnu: discrover: Remove package labels.
...
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove package
labels.
2023-05-14 13:48:01 +02:00
8ec227471a
gnu: diamond: Update to 2.1.6.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 2.1.6.
[arguments]: Do not disable tests; pass configure flag to avoid SSE4 and AVX2
in the interest of compatibility.
[license]: Set to GPLv3+.
2023-05-14 13:39:05 +02:00
6754eb339c
gnu: delly: Simplify.
...
* gnu/packages/bioinformatics.scm (delly)[source]: Simplify snippet.
[arguments]: Do not use quasiquote; simplify 'install-templates phase.
2023-05-14 13:29:34 +02:00
302e7b7820
gnu: python-pybigwig: Update to 0.3.22.
...
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.22.
[source]: Simplify snippet.
[arguments]: Explicitly disable tests; simplify 'link-with-libBigWig phase.
[build-system]: Use pyproject-build-system.
2023-05-14 13:26:21 +02:00
7e303658d7
gnu: codingquarry: Use G-expression.
...
* gnu/packages/bioinformatics.scm (codingquarry)[arguments]: Use G-expression
to simplify 'install phase. Install files to /share/codingquarry prefix.
[native-search-paths]: Adjust prefix.
[native-inputs]: Move python-2 from here...
[inputs]: ...to here.
2023-05-14 13:21:59 +02:00
68ccd1a0d8
gnu: blast+: Update to 2.14.0.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.14.0.
[arguments]: Remove trailing #T from build phases; let WHICH* return #FALSE on
failure; use G-expression.
[inputs]: Drop package labels.
2023-05-14 12:58:22 +02:00
e4ca1bcea5
gnu: jamm: Use G-expression.
...
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
2023-05-12 22:50:08 +02:00
662e2e82b1
gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY.
...
* gnu/packages/bioinformatics.scm (arriba)[arguments]:
Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop
trailing #T from build phases.
2023-05-12 22:40:18 +02:00
001d9b1c64
gnu: multichoose: Clean up.
...
* gnu/packages/bioinformatics.scm (multichoos): Fix indentation.
[arguments]: Use G-expression.
2023-05-12 22:33:44 +02:00
6d72af0747
gnu: samblaster: Update to 0.1.26.
...
* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
2023-05-12 22:31:22 +02:00
6331e41cde
gnu: samblaster: Simplify.
...
* gnu/packages/bioinformatics.scm (samblaster): Fix indentation.
[arguments]: Use G-expression; drop trailing #T from 'install phase.
[description]: Use double spacing between all sentences.
2023-05-12 22:29:38 +02:00
7da3ca1bd7
gnu: methyldackel: Update to 0.6.1.
...
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.6.1.
[arguments]: Set LIBBIGWIG variable instead of patching Makefile.
[inputs]: Replace htslib-1.9 with htslib.
2023-05-12 22:27:17 +02:00
7a199bb74c
gnu: methyldackel: Simplify arguments.
...
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop
argument list.
[native-inputs]: Drop package label.
2023-05-12 22:24:30 +02:00
5d446e439d
gnu: phast: Simplify by using G-expression.
...
* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and
drop trailing #T from build phases.
2023-05-12 22:23:23 +02:00
fac8721bfd
gnu: ribotaper: Simplify with G-expression.
...
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and
drop trailing #T from build phase.
2023-05-12 22:21:14 +02:00
0e20ed322d
gnu: sra-tools: Do link with libxml2.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use G-expression for
clarity; drop trailing #T from build phases; modify 'configure phase to
dynamically link with libxml2.
[inputs]: Drop package labels; add libxml2.
2023-05-12 21:54:01 +02:00
8ba3bf6564
gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.
...
The most important change here is the addition of the 'install-libs phase.
All other changes are just the result of switching to G-expressions.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs
phase; use G-expression; drop trailing #T from build phases.
[inputs]: Drop package labels.
2023-05-12 21:51:41 +02:00
263f235cd0
gnu: Add python-mgatk.
...
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-12 15:30:44 +02:00
42e9e8ba2e
gnu: Add homer.
...
* gnu/packages/bioinformatics.scm (homer): New variable.
2023-05-08 18:50:38 +02:00
94d0efffb3
Revert "gnu: Add python-gimmemotifs."
...
This reverts commit dc8b3ebe5d
2023-05-05 22:34:30 +02:00
dc8b3ebe5d
gnu: Add python-gimmemotifs.
...
* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
2023-05-05 15:39:29 +02:00
931650212a
gnu: Add python-biofluff.
...
* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
2023-05-05 15:39:29 +02:00
0b5088a2a3
gnu: Add python-genomepy.
...
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
2023-05-05 15:39:29 +02:00
181714e5f8
gnu: Add python-logomaker.
...
* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
2023-05-05 15:39:29 +02:00
7dc853269f
gnu: python-pyfaidx: Update to 0.7.2.1.
...
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1.
[build-system]: Use pyproject-build-system.
[arguments]: Ignore tests that require large downloads.
[native-inputs]: Remove python-six; add python-fsspec, python-pytest,
python-pytest-cov, python-mock, and python-numpy.
2023-05-05 15:39:28 +02:00
00051e8839
gnu: python-screed: Update to 1.1.2.
...
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.2.
[build-system]: Use pyproject-build-system.
[native-inputs]: Remove python-pytest.
[inputs]: Remove python-bz2file.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-04 19:28:23 +02:00
5daf470e4f
gnu: Add python-goatools.
...
* gnu/packages/bioinformatics.scm (python-goatools): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-04 19:22:04 +02:00
3f02f7d937
gnu: pigx-sars-cov-2: Update to 0.0.9.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.9.
2023-05-03 17:02:02 +02:00
83a6ca3c60
gnu: Add fanc.
...
* gnu/packages/bioinformatics.scm (fanc): New variable.
2023-05-03 11:59:54 +02:00
2b08f6874e
gnu: r-tictoc: Update to 1.2.
...
* gnu/packages/bioinformatics.scm (r-tictoc): Update to 1.2.
2023-04-29 20:28:08 +02:00
5775bbdd4b
gnu: gdcm: Disable dependent tests.
...
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
2023-04-27 16:23:22 +02:00
fa685c87ea
gnu: freebayes: Update to 1.3.7.
...
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
2023-04-27 11:40:09 +02:00
133957f7bb
gnu: vcflib: Use libwfa2.pc.
...
* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for
libwfa2.
[inputs]: Move wfa2-lib from here...
[propagated-inputs]: ...to here.
[arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name;
patch IntervalTree.h includes; add libwfa2 to pkg-config file.
2023-04-27 11:38:16 +02:00
479f2558fe
gnu: wfa2-lib: Install pkg-config file.
...
* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
2023-04-27 11:37:36 +02:00
9d82c475a3
gnu: express: Adjust bamtools location.
...
* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
#T.
2023-04-27 09:25:26 +02:00
bb385f2472
gnu: python-dendropy: Fix build.
...
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add
python-pytest.
[arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add
#:test-flags; do not delete test files.
[build-system]: Use pyproject-build-system.
2023-04-26 22:53:26 +02:00
4598928a90
gnu: cwltool: Use pyproject-build-system.
...
"setup.py install is deprecated. Use build and pip and other standards-based
tools." It then falls back to attempting to install packages via pip.
* gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use
pyproject-build-system.
2023-04-25 21:18:36 +02:00
92a903499b
gnu: python-schema-salad: Use pyproject-build-system.
...
The python-build-system fails with "setuptools.installer is
deprecated. Requirements should be satisfied by a PEP 517 installer." This,
in turn, causes all Python packages to be ignored and "pip install" to be
invoked for them.
* gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use
pyproject-build-system.
2023-04-25 21:18:35 +02:00
5a1b246736
gnu: adapterremoval: Update to 2.3.3.
...
* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
2023-04-25 19:46:29 +02:00
fc80efe1a0
gnu: bedtools-2.18: Fix build.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
2023-04-25 19:41:05 +02:00
f2e90d6f43
gnu: hisat: Build with GCC 10.
...
* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
2023-04-25 19:30:43 +02:00
0a4fa99b39
gnu: kallisto: Update to 0.48.0.
...
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0.
[arguments]: Remove trailing #T from build phase.
2023-04-25 19:28:42 +02:00
7ae5325bf1
gnu: bpp-core: Build with GCC 10.
...
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
2023-04-25 19:12:57 +02:00
2c09cc19e6
gnu: vcflib: Update to 1.0.9.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9.
[source]: Update snippet.
[inputs]: Add curl, pybind11, and wfa2-lib.
[arguments]: Adjust and reformat.
2023-04-25 19:10:19 +02:00
4ad51f5914
gnu: tabixpp: Update to 1.1.2.
...
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Simplify snippet.
[inputs]: Add curl.
[arguments]: Simplify and reformat.
2023-04-25 19:10:19 +02:00
8664c6230e
gnu: Add wfa2-lib.
...
* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
2023-04-25 19:10:18 +02:00
3a37e3ecd8
gnu: lofreq: Set file timestamps to 1980s.
...
This keeps Python from complaining: "ZIP does not support timestamps before
1980".
* gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase
'set-source-file-times-to-1980.
2023-04-25 16:17:49 +02:00
0ad4a4d155
gnu: lofreq: Drop input labels.
...
* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
2023-04-25 16:17:49 +02:00
1fca85cd88
gnu: ivar: Update to 1.4.2.
...
* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2.
[arguments]: Remove -Werror flag.
2023-04-25 16:17:49 +02:00
bca1496f72
gnu: multiqc: Update to 1.14.
...
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.14.
[build-system]: Use pyproject-build-system.
[arguments]: Simplify check phase; restore sanity-check phase.
[propagated-inputs]: Add python-rich-click.
[native-inputs]: Update test data.
2023-04-24 19:49:04 +02:00
9703ecc47b
gnu: macs: Patch version check for Python.
...
* gnu/packages/bioinformatics.scm (macs)[source]: Patch check for Python >
3.6.
2023-04-24 19:49:04 +02:00
913668e879
gnu: salmon: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (salmon): Update to 1.10.1.
[inputs]: Replace cereal-1.3.0 with cereal; add htscodecs.
[native-inputs]: Update hash of pufferfish sources.
2023-04-24 19:49:04 +02:00
b8a0a10308
gnu: Add htscodecs.
...
* gnu/packages/bioinformatics.scm (htscodecs): New variable.
2023-04-24 19:49:04 +02:00
d1252b597d
Merge remote-tracking branch 'origin/master' into core-updates
2023-04-22 09:21:22 +02:00
184658e282
gnu: bppsuite: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (bppsuite): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build.
[inputs]: Use list.
[home-page]: Changed to github page.
2023-04-21 14:01:25 +02:00
2a20acf24b
gnu: bpp-popgen: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (bpp-popgen): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21 14:01:22 +02:00
2babf3d7d7
gnu: Add maffilter.
...
* gnu/packages/bioinformatics.scm (maffilter): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-21 13:15:02 +02:00
7c75228c8b
gnu: Add bpp-phyl-omics.
...
* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
2023-04-21 12:56:39 +02:00
722a8b2296
gnu: Add bpp-seq-omics.
...
* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
2023-04-21 12:56:39 +02:00
5107a8a1a3
gnu: bpp-phyl: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
[synopsis]: Use proper capitalization.
2023-04-21 12:56:39 +02:00
627049872b
gnu: bpp-seq: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (bpp-seq): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21 12:56:38 +02:00
51ef858c94
gnu: bpp-core: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
stored sources.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21 12:56:38 +02:00
216d7bdb73
Merge remote-tracking branch 'origin/master' into core-updates
2023-04-17 19:17:39 +02:00
b95cd3f969
gnu: Add r-demuxmix.
...
* gnu/packages/bioinformatics.scm (r-demuxmix): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-17 11:16:30 +02:00
2b2068a083
gnu: Add r-demultiplex2.
...
* gnu/packages/bioinformatics.scm (r-demultiplex2): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-17 11:14:30 +02:00
3bacd3c76a
Merge branch 'master' into core-updates.
...
Conflicts:
gnu/local.mk
gnu/packages/build-tools.scm
gnu/packages/certs.scm
gnu/packages/check.scm
gnu/packages/compression.scm
gnu/packages/cups.scm
gnu/packages/fontutils.scm
gnu/packages/gnuzilla.scm
gnu/packages/guile.scm
gnu/packages/ibus.scm
gnu/packages/image-processing.scm
gnu/packages/linux.scm
gnu/packages/music.scm
gnu/packages/nss.scm
gnu/packages/pdf.scm
gnu/packages/python-xyz.scm
gnu/packages/qt.scm
gnu/packages/ruby.scm
gnu/packages/shells.scm
gnu/packages/tex.scm
gnu/packages/video.scm
gnu/packages/vulkan.scm
gnu/packages/web.scm
gnu/packages/webkit.scm
gnu/packages/wm.scm
2023-04-14 17:15:08 -04:00
acdb42e5d0
gnu: Purge pre-1.3.0 deprecated packages.
...
* gnu/packages/bioinformatics.scm (deeptools): Remove variable.
* gnu/packages/efi.scm (efi_analyzer): Ditto.
* gnu/packages/guile.scm (guile-2.2/bug-fix, guile-json): Ditto.
* gnu/packages/image.scm (libjpeg): Ditto.
* gnu/packages/kde.scm (kdevplatform): Ditto
* gnu/packages/linphone.scm (linphoneqt): Ditto.
* gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): Ditto.
* gnu/packages/mpi.scm (hwloc-2.0): Ditto.
* gnu/packages/music.scm (python-abjad, zlfo): Ditto.
* gnu/packages/perl.scm (perl-base, perl-parent): Ditto.
* gnu/packages/tryton.scm (python-trytond): Ditto.
* gnu/packages/video.scm (gnome-mpv): Ditto.
* tests/graph.scm: Use guile-json-1.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-07 17:53:37 +02:00
caf163536a
gnu: Add r-maxprobes.
...
* gnu/packages/bioinformatics.scm (r-maxprobes): New variable.
2023-03-30 14:40:01 +02:00
033955b4e8
gnu: Add r-illuminahumanmethylationepicanno-ilm10b5-hg38.
...
* gnu/packages/bioinformatics.scm
(r-illuminahumanmethylationepicanno-ilm10b5-hg38): New variable.
2023-03-30 14:38:45 +02:00
3f1617da19
gnu: Add r-cytoexplorer.
...
* gnu/packages/bioinformatics.scm (r-cytoexplorer): New variable.
2023-03-30 13:03:30 +02:00
ccb62d8feb
Merge remote-tracking branch 'origin/master' into core-updates
2023-03-20 18:49:06 +01:00
5dcbe80da8
gnu: Add transanno.
...
* gnu/packages/bioinformatics.scm (transanno): New variable.
2023-03-20 17:22:33 +01:00
4496ff34a3
gnu: Add r-conqur.
...
* gnu/packages/bioinformatics.scm (r-conqur): New variable.
2023-03-15 18:31:23 +01:00
d37b467631
gnu: r-rhandsontable: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-rhandsontable): Move this variable from
here...
* gnu/packages/cran.scm (r-rhandsontable): ...to here.
2023-03-14 17:58:28 +01:00
Ricardo Wurmus
Navid Afkhami
Efraim Flashner
Christopher Baines
Mădălin Ionel Patrașcu
Andreas Enge
Maxim Cournoyer
Bruno Victal