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
204c51cac4
gnu: Add r-premessa.
...
* gnu/packages/bioinformatics.scm (r-premessa): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-03-14 17:58:28 +01:00
27c8ab4bf3
gnu: Add r-rhandsontable.
...
* gnu/packages/bioinformatics.scm (r-rhandsontable): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2023-03-14 17:48:14 +01:00
72b1fe77b2
gnu: scvelo: Remove python-pre-commit.
...
* gnu/packages/bioinformatics.scm (scvelo)[native-inputs]: Remove
python-pre-commit.
Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
2023-03-12 11:04:06 +01:00
ed59796de5
gnu: python-doubletdetection: Remove python-pre-commit.
...
* gnu/packages/bioinformatics.scm (python-doubletdetection)[native-inputs]:
Remove python-pre-commit.
Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
2023-03-12 11:04:06 +01:00
fe9bcf9db2
gnu: Add r-plsdabatch.
...
* gnu/packages/bioinformatics.scm (r-plsdabatch): New variable.
2023-03-06 14:55:06 +01:00
7df09ee0ab
Merge remote-tracking branch 'savannah/master' into core-updates
...
Conflicts:
gnu/local.mk
gnu/packages/autotools.scm
gnu/packages/cmake.scm
gnu/packages/gnuzilla.scm
gnu/packages/haskell.scm
gnu/packages/pdf.scm
gnu/packages/python-xyz.scm
gnu/packages/samba.scm
gnu/packages/tex.scm
gnu/packages/tls.scm
gnu/packages/wxwidgets.scm
2023-03-02 10:55:08 +00:00
Ricardo Wurmus
Andreas Enge
Mădălin Ionel Patrașcu
Navid Afkhami
Maxim Cournoyer
Bruno Victal
Antero Mejr
Christopher Baines