b15e543d30
Merge branch 'master' into core-updates-frozen
2021-11-23 11:29:38 +01:00
e74bcbc64f
gnu: python-scanpy: Set PYTHONPATH variable.
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This is a follow-up to commit 664721422c
2021-11-21 09:07:50 +01:00
6c9bbf8071
gnu: python-scanpy: Update to 1.8.2.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2.
[arguments]: Disable test_clustermap test.
2021-11-21 09:07:50 +01:00
1a9665743b
gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH.
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* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
GUIX_PYTHONPATH.
2021-11-21 00:40:34 +01:00
664721422c
gnu: python-scanpy: Use GUIX_PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use
GUIX_PYTHONPATH instead of PYTHONPATH.
2021-11-21 00:39:57 +01:00
55870e86d9
gnu: multiqc: Remove sanity check.
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* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
2021-11-21 00:39:09 +01:00
e2ca652c98
gnu: multiqc: Use GUIX_PYTHONPATH.
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* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH
with GUIX_PYTHONPATH.
2021-11-21 00:39:05 +01:00
c618f4a9cc
gnu: pigx-bsseq: Update to 0.1.6.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
2021-11-20 16:31:32 +01:00
a8eea7a51e
gnu: qtltools: Fix typo.
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* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
to go" to "allows going".
2021-11-18 14:20:07 -08:00
dddc90a363
gnu: shorah: Use GUIX_PYTHONPATH in wrapper.
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* gnu/packages/bioinformatics.scm (shorah)[arguments]: Wrap executable with
GUIX_PYTHONPATH.
2021-11-18 19:25:16 +00:00
3a317f7476
Merge branch 'master' into core-updates-frozen
2021-11-17 23:43:14 +01:00
0a9a00b34c
gnu: pplacer: Fix build.
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* gnu/packages/bioinformatics.scm (pplacer): Add missing input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-11-16 15:43:51 +02:00
616bcc9c0b
gnu: python-scanpy: Run tests conditionally.
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* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
2021-11-15 15:21:06 +00:00
a0fc9e38fa
gnu: ciri-long: Move Cython to native inputs.
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* gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from
here...
[native-inputs]: ...to here.
2021-11-11 15:39:19 +00:00
c4e5fabb6e
gnu: ciri-long: Fix reference to ccs.
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* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
2021-11-11 15:39:19 +00:00
6be47c5bc5
gnu: Add circtools.
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* gnu/packages/bioinformatics.scm (circtools): New variable.
2021-11-11 15:39:19 +00:00
b8c9f061e1
gnu: Add bioparser.
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* gnu/packages/bioinformatics.scm (bioparser): New variable.
2021-11-11 15:39:19 +00:00
4052310e91
gnu: Add biosoup.
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* gnu/packages/bioinformatics.scm (biosoup): New variable.
2021-11-11 15:39:19 +00:00
1c94392a13
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-11-08 09:06:14 +02:00
d54a4285ea
gnu: bedtools-2.18: Fix build with newer toolchain.
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* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase
'compatibility, fixing syntax quirks that are problematic with newer
toolchains.
[native-inputs]: Do not inherit.
[inherit]: Do not inherit.
2021-11-03 21:07:29 +00:00
bc5155b952
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-10-31 14:49:47 +02:00
41e5c12c4a
gnu: sailfish: Use TBB 2020.
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* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
2021-10-24 21:38:25 +00:00
1bf55a4850
gnu: sailfish: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in
build phases...
[inputs]: ...and in the origin snippet of "rapmap".
2021-10-24 21:37:39 +00:00
4392783232
gnu: sailfish: Do not attempt to unpack a directory.
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patch-and-repack no longer outputs a compressed archive when the input was a
directory.
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Adjust build phase
'prepare-rapmap.
2021-10-24 21:35:57 +00:00
57c233b37b
gnu: jellyfish: Remove Ruby bindings.
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These bindings no longer build and we have no package that would need them.
* gnu/packages/bioinformatics.scm (jellyfish)[outputs]: Remove "ruby" output.
[arguments]: Remove option for building Ruby bindings.
[native-inputs]: Remove ruby.
2021-10-24 21:34:26 +00:00
da526f33f2
gnu: cutadapt: Regenerate Cython files.
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* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
2021-10-24 21:23:20 +00:00
4faca03bed
gnu: python-dnaio: Update to 0.6.0.
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* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
2021-10-24 19:47:20 +00:00
238f47c76f
gnu: macs: Fix build by setting HOME.
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* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
2021-10-24 19:09:35 +00:00
1d01043a4f
gnu: methyldackel: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
2021-10-24 19:01:22 +00:00
2820b03509
gnu: methyldackel: Pass -fcommon to compiler.
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* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
2021-10-24 19:00:53 +00:00
cc331ad7eb
gnu: flexbar: Use TBB 2020.
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* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
2021-10-24 18:50:09 +00:00
084bdf9d69
gnu: flexbar: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
2021-10-24 18:49:43 +00:00
d0a1d798ee
gnu: bwa: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
2021-10-24 18:48:53 +00:00
2da99b671e
gnu: bwa: Pass -fcommon to compiler.
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* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
2021-10-24 18:48:20 +00:00
724972bcca
gnu: bowtie1: Use TBB 2020.
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* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
2021-10-24 18:47:45 +00:00
f336cc4fe7
gnu: bowtie: Replace invalid characters.
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* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
2021-10-24 18:44:57 +00:00
e5a26a1f02
gnu: bowtie: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
2021-10-24 16:59:39 +00:00
2ec601580b
gnu: bowtie: Use TBB 2020.
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* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
2021-10-24 16:58:58 +00:00
973b21aa6a
gnu: Add r-umi4cpackage.
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* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
2021-10-24 13:45:46 +00:00
42873c2b06
gnu: tbb-for-salmon: Rename.
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* gnu/packages/tbb.scm (tbb-for-salmon): Rename this variable...
(tbb-2020): ...to this.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Rename it.
2021-10-24 13:28:05 +00:00
4a0cd6297a
gnu: Add qtltools.
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* gnu/packages/bioinformatics.scm (qtltools): New variable.
2021-10-22 21:29:25 +00:00
a8bac123f0
gnu: Add gdc-client.
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* gnu/packages/bioinformatics.scm (gdc-client): New variable.
2021-10-21 14:49:01 +00:00
f65917f607
gnu: Add r-shaman.
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* gnu/packages/bioinformatics.scm (r-shaman): New variable.
2021-10-21 14:34:35 +00:00
4885f40b80
gnu: Add r-misha.
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* gnu/packages/bioinformatics.scm (r-misha): New variable.
2021-10-21 14:25:44 +00:00
42c9b75b25
gnu: Add ciri-long.
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* gnu/packages/bioinformatics.scm (ciri-long): New variable.
2021-10-21 13:39:36 +00:00
10664fcc8c
gnu: python-biopython: Update to 1.76.
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* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.76.
(python-biopython-1.73): New variable.
(instrain)[inputs]: Replace python-biopython with python-biopython-1.73.
2021-10-21 13:33:51 +00:00
36cf0253a9
gnu: instrain: Update to 1.5.4.
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* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
2021-10-21 13:32:37 +00:00
57841a91f5
gnu: Add python-bwapy.
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* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
2021-10-21 12:23:25 +00:00
6526c35df5
gnu: Add python-pyspoa.
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* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
2021-10-21 12:23:22 +00:00
174c29a8e0
gnu: salmon: Use older version of TBB.
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* gnu/packages/bioinformatics.scm (salmon)[arguments]: Define
HAVE_NUMERIC_LIMITS128; compute TBB_VERSION.
[inputs]: Replace tbb with tbb-for-salmon.
2021-10-19 06:28:30 +00:00
Ludovic Courtès
Ricardo Wurmus
Vagrant Cascadian
Julien Lepiller
Efraim Flashner