Ricardo Wurmus
a4e7475edc
gnu: rsem: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
2021-12-04 15:27:39 +01:00
Ricardo Wurmus
c45c909026
gnu: rsem: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:26:48 +01:00
Ricardo Wurmus
5e0bcba57b
gnu: rsem: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
2021-12-04 15:26:01 +01:00
Ricardo Wurmus
23975fe27a
gnu: rsem: Remove trailing #T from snippet.
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* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
2021-12-04 15:25:26 +01:00
Ricardo Wurmus
cfaf37d10b
gnu: prodigal: Remove reference to %outputs.
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* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:13:11 +01:00
Ricardo Wurmus
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase.
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* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
2021-12-04 15:11:28 +01:00
Ricardo Wurmus
e128839a94
gnu: prank: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:11:04 +01:00
Ricardo Wurmus
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
2021-12-04 12:42:51 +01:00
Ricardo Wurmus
114eb987cb
gnu: mash: Replace references to %build-inputs.
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* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
2021-12-04 00:32:01 +01:00
Ricardo Wurmus
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs.
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* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
2021-12-04 00:31:20 +01:00
Ricardo Wurmus
a6b6084649
gnu: mash: Simplify snippet.
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* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04 00:30:44 +01:00
Ricardo Wurmus
31409a4af7
gnu: mafft: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
2021-12-04 00:22:27 +01:00
Ricardo Wurmus
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs.
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* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
2021-12-04 00:21:27 +01:00
Ricardo Wurmus
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04 00:19:08 +01:00
Ricardo Wurmus
7c2ee27360
gnu: fastp: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04 00:16:10 +01:00
Ricardo Wurmus
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs.
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* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
2021-12-04 00:06:43 +01:00
Ricardo Wurmus
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
2021-12-04 00:03:54 +01:00
Ricardo Wurmus
62e0641892
gnu: fxtract: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04 00:02:20 +01:00
Ricardo Wurmus
4f03151ca4
gnu: delly: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-04 00:00:26 +01:00
Ricardo Wurmus
3601fcbf65
gnu: libbigwig: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:57:24 +01:00
Ricardo Wurmus
fd607a9efa
gnu: cd-hit: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
2021-12-03 23:56:11 +01:00
Ricardo Wurmus
c40852a227
gnu: bowtie1: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-03 23:54:10 +01:00
Ricardo Wurmus
a47a90b900
gnu: bowtie: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:52:43 +01:00
Ricardo Wurmus
f5c38ee45f
gnu: bless: Remove reference to %build-inputs.
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* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp. Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
2021-12-03 23:51:16 +01:00
Ricardo Wurmus
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases.
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* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
2021-12-03 23:48:46 +01:00
Ricardo Wurmus
0e09065460
gnu: bedtools: Remove reference to %outputs.
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* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
2021-12-03 23:36:18 +01:00
Ricardo Wurmus
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
2021-12-03 23:26:48 +01:00
Ricardo Wurmus
ce9bfcddb5
gnu: imp: Update to 2.15.0.
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* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
2021-12-03 22:29:52 +01:00
Ricardo Wurmus
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0.
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* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
2021-12-03 14:55:38 +01:00
Ricardo Wurmus
d0aa14a43d
gnu: Add vbz-compression.
...
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
Ricardo Wurmus
6d4f260166
gnu: bamutils: Update to 1.0.14.
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* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
2021-12-03 13:56:02 +01:00
Ricardo Wurmus
673cc29908
gnu: bamutils: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus
361e0d9f27
gnu: bamm: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus
7fb5bfc54f
gnu: python-plastid: Update to 0.5.1.
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* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus
b7aaf6c418
gnu: ivar: Disable parallel tests.
...
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
Ricardo Wurmus
aa2d5ca02e
gnu: Remove python2-biom-format.
...
There are no users of this variant, and the current version of biom-format
does not support Python 2.
* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
2021-12-03 13:31:32 +01:00
Ricardo Wurmus
a2423c0ca4
gnu: ribodiff: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
2021-12-02 18:32:33 +01:00
Ricardo Wurmus
1123d25830
gnu: ribodiff: Disable broken test.
...
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
2021-12-02 18:32:10 +01:00
Ricardo Wurmus
31d372cd8a
gnu: khmer: Fix build with Python 3.8.
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* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
2021-12-02 18:24:31 +01:00
Ricardo Wurmus
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10.
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* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
2021-12-02 18:02:07 +01:00
Ricardo Wurmus
28ad55a59d
gnu: pardre: Update to 2.2.5.
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* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
2021-12-02 15:40:46 +01:00
Ricardo Wurmus
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI.
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* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
2021-12-02 15:40:46 +01:00
Ricardo Wurmus
a8fff63daa
gnu: Add python-mygene.
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* gnu/packages/bioinformatics.scm (python-mygene): New variable.
2021-12-02 11:57:28 +01:00
Ricardo Wurmus
b15a525703
gnu: Add python-biothings-client.
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* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
2021-12-02 11:57:13 +01:00
Ricardo Wurmus
37c475ebc0
gnu: prinseq: Fix use of SEARCH-INPUT-FILE.
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* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
2021-12-02 11:26:55 +01:00
Ricardo Wurmus
d53679c531
gnu: Remove couger.
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This package has been moved to the Guix Past channel.
* gnu/packages/bioinformatics.scm (couger): Remove variable.
2021-12-02 00:32:12 +01:00
Ricardo Wurmus
173a2998d9
gnu: r-umi4cpackage: Embed references to perl and bowtie2.
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* gnu/packages/bioinformatics.scm (r-umi4cpackage)[arguments]: Add build
phases to patch calls of bowtie2 and perl.
[inputs]: Add perl and bowtie.
[synopsis]: Remove trailing period.
2021-11-30 16:46:17 +01:00
Ludovic Courtès
b15e543d30
Merge branch 'master' into core-updates-frozen
2021-11-23 11:29:38 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
6c9bbf8071
gnu: python-scanpy: Update to 1.8.2.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2.
[arguments]: Disable test_clustermap test.
2021-11-21 09:07:50 +01:00
