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3290 Commits

Author SHA1 Message Date
Ricardo Wurmus
2da567d137
gnu: python-cooler: Use python-cytoolz-for-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz with python-cytoolz-for-cooler.
 2021-12-07 13:24:58 +01:00
Ricardo Wurmus
899121f4d6
gnu: phylip: Update to 3.697. 
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
 2021-12-07 13:05:53 +01:00
Ricardo Wurmus
e86fe9801e
gnu: phylip: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
 2021-12-07 13:05:35 +01:00
Ricardo Wurmus
125fdc3ba4
gnu: phylip: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
 2021-12-07 13:05:15 +01:00
Ricardo Wurmus
4561ca7f4e
gnu: subread: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
 2021-12-07 12:59:51 +01:00
Ricardo Wurmus
96b2be833d
gnu: subread: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
 2021-12-07 12:59:36 +01:00
Ricardo Wurmus
9a03587b62
gnu: subread: Update home page.. 
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
 2021-12-07 12:55:08 +01:00
Ricardo Wurmus
aa25c9b1a4
gnu: subread: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
 2021-12-07 12:54:48 +01:00
Ricardo Wurmus
06fca01968
gnu: hisat: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
 2021-12-07 11:51:10 +01:00
Ricardo Wurmus
2f7287b3a7
gnu: hisat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
9dc727f827
gnu: hisat: Remove invalid characters. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
478e3e714a
gnu: crossmap: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b5c9afb7c5
gnu: Remove python2-bx-python. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
699b443c86
gnu: python-bx-python: Update to 0.8.12. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12.
[propagated-inputs]: Remove python-six.
[arguments]: Remove.  Tests are still not run, though.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
4b4ab4ce4d
gnu: Remove pbtranscript-tofu. 
Upstream has disappeared and it depends on Python 2, which is no longer
supported.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b452d7c2cf
gnu: python-pyfit-sne: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
ca2f851da1
gnu: f-seq: Update name of commons-cli JAR. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
f0763fba5c
gnu: f-seq: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
1310879fb0
gnu: f-seq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
9bc0f45df5
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-12-05 19:17:41 +01:00
Ricardo Wurmus
6db3c536e8
gnu: python-bwapy: Remove sanity-check. 
* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase
'relax-requirements to accept a slightly older version of wheel; remove the
'sanity-check phase.
 2021-12-05 17:38:15 +01:00
Ricardo Wurmus
dd67154e5d
gnu: Remove python2-plastid. 
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
 2021-12-05 17:37:05 +01:00
Ricardo Wurmus
98264531be
gnu: Remove python2-twobitreader. 
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
 2021-12-05 17:36:43 +01:00
Ricardo Wurmus
4202f4d58a
gnu: python-bbknn: Fix sanity-check phase. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.
 2021-12-05 17:33:17 +01:00
Ricardo Wurmus
b1bd997d50
gnu: python-bbknn: Add missing input. 
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
 2021-12-05 17:32:50 +01:00
Ricardo Wurmus
19f6b770dc
gnu: velvet: Add missing TeX package. 
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-05 17:22:11 +01:00
Ricardo Wurmus
fe0f8c627a
gnu: velvet: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
 2021-12-05 17:21:39 +01:00
Ricardo Wurmus
f2b99e3aaf
gnu: python-bwapy: Remove pre-built object files. 
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
57f278ffc4
gnu: metabat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
8ae33d6844
gnu: kraken2: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
c973107a25
gnu: methyldackel: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
d531dc6761
gnu: phast: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
2b1e53850f
gnu: libsbml: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
dc4b4d4d95
gnu: ataqv: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to
%outputs and %build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
03ca627b09
gnu: adapterremoval: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove
reference to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
fac4c98699
gnu: bbmap: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
b798d90bee
gnu: intervaltree: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
c9892edceb
gnu: biobambam2: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
a8b60bd475
gnu: sjcount: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
4c6cb448fd
gnu: sjcount: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
c1fe074915
gnu: dropseq-tools: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference
to %build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
1462e5c919
gnu: dropseq-tools: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove
trailing #T from build phases...
[source]: ...and from the snippet.
 2021-12-05 15:04:02 +01:00
Marius Bakke
db5646d957
gnu: Adjust for python-build-system behavior change. 
Commit cb72f9a773 changed the semantics of
SITE-PACKAGES, but did not adjust all callers.

* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for
missing trailing slash.
* gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
 2021-12-05 14:02:10 +01:00
Marius Bakke
b507cc49ab
gnu: python-pyvcf: Fix bytecode compilation. 
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to
patch sample script.
 2021-12-05 14:02:10 +01:00
Efraim Flashner
e70e26423b
gnu: minimap2: Update to 2.23. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
 2021-12-05 11:51:10 +02:00
Ricardo Wurmus
1e7bd5e679
gnu: salmon: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove
reference to %build-inputs.
 2021-12-05 00:49:06 +01:00
Ricardo Wurmus
98d2abe523
gnu: sailfish: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove
references to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
39e2a84f52
gnu: sailfish: Simplify snippet. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
b0fd09f856
gnu: piranha: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove
references to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
01d2e2b334
gnu: piranha: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T
from build phases.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
502538c6e4
gnu: emboss: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove
reference to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
2657bdc100
gnu: vcftools: Replace references to %outputs. 
* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove
references to %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
eec1bdcd9e
gnu: seqan-1: Use gexp for builder. 
* gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
2c1c75a56c
gnu: seqan-2: Use gexp for builder. 
* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
f41576c09f
gnu: sra-tools: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead
of referencing %build-inputs.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
f33e490334
gnu: preseq: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to
%outputs and %build-inputs by using a gexp.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
8a446f5e41
gnu: preseq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
cc491eab7e
gnu: plink-ng: Enable tests. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
 2021-12-04 16:00:08 +01:00
Ricardo Wurmus
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:35:28 +01:00
Ricardo Wurmus
88bb81b515
gnu: plink: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
 2021-12-04 15:31:31 +01:00
Ricardo Wurmus
e920101141
gnu: plink: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 15:31:08 +01:00
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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
 2021-12-04 00:30:44 +01:00
Ricardo Wurmus
31409a4af7
gnu: mafft: Remove trailing #T. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
 2021-12-02 11:57:28 +01:00
Ricardo Wurmus
b15a525703
gnu: Add python-biothings-client. 
* 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. 
* 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. 
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. 
* 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. 
This is a follow-up to commit 664721422c.

* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Set PYTHONPATH
variable during the build as GUIX_PYTHONPATH does not have the intended
effect.
 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
Ricardo Wurmus
1a9665743b
gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
GUIX_PYTHONPATH.
 2021-11-21 00:40:34 +01:00
Ricardo Wurmus
664721422c
gnu: python-scanpy: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use
GUIX_PYTHONPATH instead of PYTHONPATH.
 2021-11-21 00:39:57 +01:00
Ricardo Wurmus
55870e86d9
gnu: multiqc: Remove sanity check. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
 2021-11-21 00:39:09 +01:00
Ricardo Wurmus
e2ca652c98
gnu: multiqc: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH
with GUIX_PYTHONPATH.
 2021-11-21 00:39:05 +01:00
Ricardo Wurmus
c618f4a9cc
gnu: pigx-bsseq: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
 2021-11-20 16:31:32 +01:00
Vagrant Cascadian
a8eea7a51e
gnu: qtltools: Fix typo. 
* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
  to go" to "allows going".
 2021-11-18 14:20:07 -08:00
Ricardo Wurmus
dddc90a363
gnu: shorah: Use GUIX_PYTHONPATH in wrapper. 
* gnu/packages/bioinformatics.scm (shorah)[arguments]: Wrap executable with
GUIX_PYTHONPATH.
 2021-11-18 19:25:16 +00:00
Ludovic Courtès
3a317f7476
Merge branch 'master' into core-updates-frozen 2021-11-17 23:43:14 +01:00
Julien Lepiller
0a9a00b34c
gnu: pplacer: Fix build. 
* 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
Ricardo Wurmus
616bcc9c0b
gnu: python-scanpy: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
 2021-11-15 15:21:06 +00:00
Ricardo Wurmus
a0fc9e38fa
gnu: ciri-long: Move Cython to native inputs. 
* gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from
here...
[native-inputs]: ...to here.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
c4e5fabb6e
gnu: ciri-long: Fix reference to ccs. 
* 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
Ricardo Wurmus
6be47c5bc5
gnu: Add circtools. 
* gnu/packages/bioinformatics.scm (circtools): New variable.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
b8c9f061e1
gnu: Add bioparser. 
* gnu/packages/bioinformatics.scm (bioparser): New variable.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
4052310e91
gnu: Add biosoup. 
* gnu/packages/bioinformatics.scm (biosoup): New variable.
 2021-11-11 15:39:19 +00:00
Efraim Flashner
1c94392a13
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-11-08 09:06:14 +02:00
Ricardo Wurmus
d54a4285ea
gnu: bedtools-2.18: Fix build with newer toolchain. 
* 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
Efraim Flashner
bc5155b952
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-10-31 14:49:47 +02:00
Ricardo Wurmus
41e5c12c4a
gnu: sailfish: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 21:38:25 +00:00
Ricardo Wurmus
1bf55a4850
gnu: sailfish: Remove trailing #T. 
* 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
Ricardo Wurmus
4392783232
gnu: sailfish: Do not attempt to unpack a directory. 
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
Ricardo Wurmus
57c233b37b
gnu: jellyfish: Remove Ruby bindings. 
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
Ricardo Wurmus
da526f33f2
gnu: cutadapt: Regenerate Cython files. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
 2021-10-24 21:23:20 +00:00
Ricardo Wurmus
4faca03bed
gnu: python-dnaio: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
 2021-10-24 19:47:20 +00:00
Ricardo Wurmus
238f47c76f
gnu: macs: Fix build by setting HOME. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
 2021-10-24 19:09:35 +00:00
Ricardo Wurmus
1d01043a4f
gnu: methyldackel: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
 2021-10-24 19:01:22 +00:00
Ricardo Wurmus
2820b03509
gnu: methyldackel: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
 2021-10-24 19:00:53 +00:00
Ricardo Wurmus
cc331ad7eb
gnu: flexbar: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:50:09 +00:00
Ricardo Wurmus
084bdf9d69
gnu: flexbar: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
 2021-10-24 18:49:43 +00:00
Ricardo Wurmus
d0a1d798ee
gnu: bwa: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
 2021-10-24 18:48:53 +00:00
Ricardo Wurmus
2da99b671e
gnu: bwa: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
 2021-10-24 18:48:20 +00:00
Ricardo Wurmus
724972bcca
gnu: bowtie1: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:47:45 +00:00
Ricardo Wurmus
f336cc4fe7
gnu: bowtie: Replace invalid characters. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
 2021-10-24 18:44:57 +00:00
Ricardo Wurmus
e5a26a1f02
gnu: bowtie: Remove trailing #T. 
* 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
Ricardo Wurmus
2ec601580b
gnu: bowtie: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
 2021-10-24 16:58:58 +00:00
Ricardo Wurmus
973b21aa6a
gnu: Add r-umi4cpackage. 
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
 2021-10-24 13:45:46 +00:00
Ricardo Wurmus
42873c2b06
gnu: tbb-for-salmon: Rename. 
* 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
Ricardo Wurmus
4a0cd6297a
gnu: Add qtltools. 
* gnu/packages/bioinformatics.scm (qtltools): New variable.
 2021-10-22 21:29:25 +00:00
Ricardo Wurmus
a8bac123f0
gnu: Add gdc-client. 
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
 2021-10-21 14:49:01 +00:00
Ricardo Wurmus
f65917f607
gnu: Add r-shaman. 
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
 2021-10-21 14:34:35 +00:00
Ricardo Wurmus
4885f40b80
gnu: Add r-misha. 
* gnu/packages/bioinformatics.scm (r-misha): New variable.
 2021-10-21 14:25:44 +00:00
Ricardo Wurmus
42c9b75b25
gnu: Add ciri-long. 
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
 2021-10-21 13:39:36 +00:00
Ricardo Wurmus
10664fcc8c
gnu: python-biopython: Update to 1.76. 
* 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
Ricardo Wurmus
36cf0253a9
gnu: instrain: Update to 1.5.4. 
* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
 2021-10-21 13:32:37 +00:00
Ricardo Wurmus
57841a91f5
gnu: Add python-bwapy. 
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
 2021-10-21 12:23:25 +00:00
Ricardo Wurmus
6526c35df5
gnu: Add python-pyspoa. 
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
 2021-10-21 12:23:22 +00:00
Ricardo Wurmus
174c29a8e0
gnu: salmon: Use older version of TBB. 
* 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
Mathieu Othacehe
a1eca979fb
Merge remote-tracking branch 'origin/master' into core-updates-frozen. 2021-10-12 17:46:23 +00:00
Felix Gruber
9101c7bf8e
gnu: clipper: Disable non-deterministic test. 
This test fails/succeeds non-deterministically.

* gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable
  non-deterministic test test_get_FDR_cutoff_mean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-10-12 18:13:29 +02:00
Lars-Dominik Braun
c8a7ba621b
gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:55 +02:00
Lars-Dominik Braun
26488f63b8
gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:55 +02:00
Lars-Dominik Braun
07f2e4993b
gnu: pigx-chipseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun
e51a3f4a72
gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun
fb1ffc53ba
gnu: pigx-bsseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun
7eb9fe4e53
gnu: ngless: Fix build. 
Apply upstream patch to restore compatibility with current Stackage.

* gnu/packages/patches/ngless-unliftio.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bioinformatics.scm (ngless): Use it.
 2021-10-08 09:13:53 +02:00
Lars-Dominik Braun
b97f549b14
gnu: Update Haskell ecosystem. 
Bump packages’ versions to the lastest Stackage or Hackage
release. Since packages are interdependent, do so in a single commit.

525 packages have been updated.

These packages have been removed, because they fail to build, have no
newer version available and no dependencies:

corrode
ghc-easytest
ghc-edisonapi
ghc-edisoncore
ghc-pandoc-types
ghc-regex-tdfa-text

These have been removed, because they are no longer required:

ghc-happy-1.19.9
ghc-prettyprinter-1.6
ghc-protolude-0.3

ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc
does not use them any more.

Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
 2021-10-08 09:13:52 +02:00
Ricardo Wurmus
53611ab5c5
gnu: pigx-chipseq: Update to 0.0.53. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
 2021-09-29 09:58:45 +02:00
Charles
f36b789f78
gnu: Update some packages using old JavaScript minifier. 
* gnu/packages/minetest.scm (minetest-basic-trains): New variable.
* gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input.
* gnu/packages/ci.scm (laminar): Update uglifyjs input.
* gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker
r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input.
* gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-09-22 16:03:19 +03:00
zimoun
f80824fe09
gnu: Add r-presto. 
* gnu/packages/bioinformatics.scm (r-presto): New variable.
 2021-09-20 17:23:16 +02:00
Ricardo Wurmus
0406f1c2e1
gnu: discrover: Update package name in texlive-union. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
 2021-09-13 22:49:56 +02:00
Ludovic Courtès
d9dfbf886d
Merge branch 'master' into core-updates-frozen 2021-09-07 14:19:08 +02:00
Ludovic Courtès
b949f34f31
gnu: Use the non-deprecated TeX packages. 
This commit leaves 'dblatex' and 'texlive-hyperref' as users of
deprecated packages, but these have many dependents.

* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use
non-deprecated TeX Live packages.
(velvet)[native-inputs]: Likewise.
* gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise.
(chez-web)[native-inputs]: Likewise.
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise.
* gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise.
* gnu/packages/maths.scm (hypre)[native-inputs]: Likewise.
* gnu/packages/music.scm (lilypond)[native-inputs]: Likewise.
* gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise.
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]:
Likewise.
(python-matplotlib-documentation)[native-inputs]: Likewise.
(python-ipython-documentation)[native-inputs]: Likewise.
(python-nbconvert)[native-inputs]: Likewise.
(python-pypandoc)[native-inputs]: Likewise.
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise.
* gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise.
(teximpatient)[native-inputs]: Likewise.
(texlive-latex-pgf)[propagated-inputs]: Likewise.
(texlive-beamer)[propagated-inputs]: Likewise.
 2021-09-06 22:02:15 +02:00
Ricardo Wurmus
c82b723bf8
gnu: Add megadepth. 
* gnu/packages/bioinformatics.scm (megadepth): New variable.
 2021-09-06 14:48:24 +02:00
Felix Gruber
93bf42361c
gnu: Replace PYTHONPATH with GUIX_PYTHONPATH. 
In packages that do not use python-build-system, PYTHONPATH is generally
not defined. Instead we can use GUIX_PYTHONPATH which should contain all
Python dependencies.

* gnu/packages/bioinformatics.scm (shorah)[arguments]: Replace
  PYTHONPATH with GUIX_PYTHONPATH.
* gnu/packages/debug.scm (c-vise)[arguments]: Idem.
* gnu/packages/gnome.scm (drawing, apostrophe, ocrfeeder)[arguments]: Idem.
* gnu/packages/music.scm (a2jmidid)[arguments]: Idem.
* gnu/packages/syndication.scm (gfeeds)[arguments]: Idem.
* gnu/packages/xdisorg.scm (gammastep)[arguments]: Idem.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-09-06 10:47:54 +02:00
Ricardo Wurmus
c75b30d58f
gnu: Add r-catch. 
* gnu/packages/bioinformatics.scm (r-catch): New variable.
 2021-09-01 14:53:36 +02:00
Ricardo Wurmus
4abf226833
gnu: Add scregseg. 
* gnu/packages/bioinformatics.scm (scregseg): New variable.
 2021-08-31 23:11:06 +02:00
Ricardo Wurmus
a1ee212184
gnu: python-strawc: Propagate pybind11. 
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Ricardo Wurmus
55cb5a62a1
gnu: python-scanpy: Propagate sinfo. 
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Marius Bakke
c4133c43c7
Merge branch 'master' into core-updates-frozen 
Conflicts:
	gnu/packages/algebra.scm
	gnu/packages/games.scm
	gnu/packages/golang.scm
	gnu/packages/kerberos.scm
	gnu/packages/mail.scm
	gnu/packages/python.scm
	gnu/packages/ruby.scm
	gnu/packages/scheme.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
 2021-08-12 00:30:27 +02:00
Marius Bakke
b029be2ee0
Merge branch 'master' into core-updates-frozen 
Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/cmake.scm
	gnu/packages/curl.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/gpodder.scm
	gnu/packages/music.scm
	gnu/packages/patches/glibc-bootstrap-system.patch
	gnu/packages/python-xyz.scm
	gnu/packages/shells.scm
	gnu/packages/statistics.scm
 2021-07-29 22:34:57 +02:00
Ricardo Wurmus
7712154ccb
gnu: Add python-coolbox. 
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus
b105655670
gnu: python-scanpy: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus
d84ead8174
gnu: Add python-dna-features-viewer. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus
e85b35070c
gnu: Add python-pybbi. 
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus
db13eb962f
gnu: Add python-strawc. 
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus
17c765e2e1
gnu: Add r-cytonorm. 
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus
f66759e0b2
gnu: Add ivar. 
* gnu/packages/bioinformatics.scm (ivar): New variable.
 2021-08-25 11:22:02 +02:00
Ricardo Wurmus
27952318a5
gnu: fastp: Update to 0.20.1. 
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
 2021-08-20 10:49:48 +02:00
Ricardo Wurmus
907f835e19
gnu: pigx-rnaseq: Update to 0.0.18. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
 2021-08-11 19:33:38 +02:00
Ricardo Wurmus
a79ad5fce5
gnu: pigx-rnaseq: Update to 0.0.19. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
 2021-08-13 15:23:39 +02:00
Ricardo Wurmus
f1b64c435a
gnu: pigx-sars-cov2-ww: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
 2021-08-05 16:46:34 +02:00
Ricardo Wurmus
2ab5d08fbe
gnu: Add r-spectre. 
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
 2021-08-03 10:43:08 +02:00
Ricardo Wurmus
3e5eff8c30
gnu: Add seqan 3. 
* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
 2021-07-26 11:54:21 +02:00
Ricardo Wurmus
99ca1ae4f8
gnu: Add segemehl. 
* gnu/packages/bioinformatics.scm (segemehl): New variable.
 2021-07-26 11:08:13 +02:00
Ludovic Courtès
d468a03a00
gnu: Use 'search-input-directory' and 'search-input-file' where appropriate. 
This changes some of the remaining uses of this idiom:

  (string-append (assoc-ref inputs "LABEL") "FILE")

to one of:

  (search-input-file inputs "FILE")
  (search-input-directory inputs "FILE")

* gnu/packages/axoloti.scm (axoloti-patcher): Use
'search-input-directory'.
(axoloti-patcher-next): Likewise.
* gnu/packages/bioinformatics.scm (java-picard): Likewise.
* gnu/packages/bootloaders.scm (grub-hybrid): Likewise.
(u-boot-puma-rk3399): Likewise.
(u-boot-rock64-rk3328): Likewise.
(u-boot-firefly-rk3399): Likewise.
(u-boot-rockpro64-rk3399): Likewise.
(u-boot-pinebook-pro-rk3399): Likewise.
* gnu/packages/cran.scm (r-shiny): Likewise.
(r-shinytree): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Likewise.
(emacs-rime): Likewise.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/games.scm (bsd-games): Likewise.
(seahorse-adventures): Likewise.
(einstein): Likewise.
* gnu/packages/gimp.scm (gimp-fourier): Likewise.
* gnu/packages/gnome.scm (gspell): Likewise.
* gnu/packages/guile-xyz.scm (guile-libyaml): Likewise.
* gnu/packages/java.scm (icedtea-7): Likewise.
* gnu/packages/language.scm (nimf): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (claws-mail): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/scheme.scm (scm): Likewise.
* gnu/packages/security-token.scm (python-fido2): Likewise.
* gnu/packages/syndication.scm (rtv): Likewise.
* gnu/packages/tls.scm (acme-client): Likewise.
* gnu/packages/web.scm (netsurf): Likewise.
* gnu/packages/wine.scm (wine-staging): Likewise.
* gnu/packages/wxwidgets.scm (wxwidgets): Likewise.
 2021-07-24 16:23:24 +02:00
Ludovic Courtès
828cfdc47e
gnu: Use 'search-input-file' when looking for .jar files. 
* gnu/packages/bioinformatics.scm (java-picard-1.113): Use
'search-input-file' when looking for *.jar.
(fastqc): Likewise.
* gnu/packages/groovy.scm (groovy): Likewise.
* gnu/packages/java.scm (ant-bootstrap): Likewise.
(ecj-bootstrap): Likewise.
(java-cisd-base): Likewise.
(java-cisd-args4j): Likewise.
(java-cisd-jhdf5): Likewise.
(java-native-access): Likewise.
(java-native-access-platform): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès
bc64d9554b
gnu: Use 'search-input-file' when looking for executables. 
* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when
looking for executables.
* gnu/packages/audio.scm (ableton-link): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (roary): Likewise.
(ngless): Likewise.
* gnu/packages/boost.scm (boost-for-irods): Likewise.
* gnu/packages/bootloaders.scm (grub): Likewise.
(grub-efi): Likewise.
* gnu/packages/chemistry.scm (inchi): Likewise.
* gnu/packages/dictionaries.scm (ding): Likewise.
* gnu/packages/dlang.scm (ldc): Likewise.
* gnu/packages/education.scm (childsplay): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise.
(emacs-haskell-mode): Likewise.
(emacs-auctex): Likewise.
(emacs-ggtags): Likewise.
(emacs-graphviz-dot-mode): Likewise.
(emacs-flycheck-grammalecte): Likewise.
(emacs-counsel-notmuch): Likewise.
(emacspeak): Likewise.
(emacs-exwm): Likewise.
(emacs-exwm-x): Likewise.
(emacs-treemacs): Likewise.
(emacs-telega): Likewise.
(emacs-exiftool): Likewise.
* gnu/packages/emulators.scm (higan): Likewise.
* gnu/packages/engineering.scm (freehdl): Likewise.
(librepcb): Likewise.
* gnu/packages/entr.scm (entr): Likewise.
* gnu/packages/file-systems.scm (libeatmydata): Likewise.
(xfstests): Likewise.
(mergerfs): Likewise.
(mergerfs-tools): Likewise.
* gnu/packages/finance.scm (monero-gui): Likewise.
* gnu/packages/flashing-tools.scm (flashrom): Likewise.
* gnu/packages/fontutils.scm (fontforge): Likewise.
* gnu/packages/game-development.scm (python2-renpy): Likewise.
* gnu/packages/games.scm (opensurge): Likewise.
(xboard): Likewise.
(hyperrogue): Likewise.
(flare-game): Likewise.
(chessx): Likewise.
* gnu/packages/geo.scm (grass): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/gnome.scm (mm-common): Likewise.
(network-manager-openvpn): Likewise.
(network-manager-vpnc): Likewise.
(network-manager-openconnect): Likewise.
(apostrophe): Likewise.
* gnu/packages/gnupg.scm (pius): Likewise.
(jetring): Likewise.
* gnu/packages/gnuzilla.scm (icedove): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
* gnu/packages/graphviz.scm (xdot): Likewise.
* gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise.
* gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise.
* gnu/packages/ibus.scm (ibus): Likewise.
* gnu/packages/image.scm (phockup): Likewise.
* gnu/packages/irc.scm (quassel): Likewise.
* gnu/packages/java.scm (drip): Likewise.
(ant-bootstrap): Likewise.
(tla2tools): Likewise.
* gnu/packages/julia.scm (julia): Likewise.
* gnu/packages/less.scm (lesspipe): Likewise.
* gnu/packages/libreoffice.scm (libreoffice): Likewise.
* gnu/packages/linux.scm (fuse): Likewise.
(lm-sensors): Likewise.
(bluez): Likewise.
(fakeroot): Likewise.
(inputattach): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise.
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise.
* gnu/packages/lua.scm (fennel): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (public-inbox): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
(maxima): Likewise.
(frama-c): Likewise.
* gnu/packages/messaging.scm (libgadu): Likewise.
* gnu/packages/music.scm (denemo): Likewise.
(curseradio): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
(squid): Likewise.
(aircrack-ng): Likewise.
* gnu/packages/node.scm (node): Likewise.
(node-llparse-frontend-bootstrap): Likewise.
(node-llparse-bootstrap): Likewise.
(llhttp-bootstrap): Likewise.
(node-lts): Likewise.
* gnu/packages/ocaml.scm (ocaml-4.11): Likewise.
(opam): Likewise.
(ocaml-graph): Likewise.
* gnu/packages/orpheus.scm (orpheus): Likewise.
* gnu/packages/password-utils.scm (password-store): Likewise.
* gnu/packages/python.scm (pypy3): Likewise.
* gnu/packages/qt.scm (qt5ct): Likewise.
* gnu/packages/radio.scm (libosmo-dsp): Likewise.
* gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise.
* gnu/packages/rust.scm (rust-1.30): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/suckless.scm (surf): Likewise.
* gnu/packages/syndication.scm (gfeeds): Likewise.
* gnu/packages/telephony.scm (mumble): Likewise.
* gnu/packages/terminals.scm (alacritty): Likewise.
* gnu/packages/tex.scm (texlive-bin): Likewise.
* gnu/packages/uml.scm (plantuml): Likewise.
* gnu/packages/version-control.scm (python-git-multimail): Likewise.
(gitolite): Likewise.
(hg-commitsigs): Likewise.
(git-when-merged): Likewise.
(git-imerge): Likewise.
(gita): Likewise.
* gnu/packages/video.scm (you-get): Likewise.
* gnu/packages/vim.scm (eovim): Likewise.
* gnu/packages/virtualization.scm (qemu): Likewise.
(virt-manager): Likewise.
(criu): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
(xl2tpd): Likewise.
* gnu/packages/wm.scm (i3lock-fancy): Likewise.
* gnu/packages/wxwidgets.scm (python-wxpython): Likewise.
(python2-wxpython): Likewise.
* gnu/packages/xdisorg.scm (autorandr): Likewise.
* gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise.
(v86d): Likewise.
(mkfontdir): Likewise.
(xpra): Likewise.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès
377e9453ca
gnu: Use 'search-input-file' when looking for *.so and *.a. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-file' when looking for *.a and *.so.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/engineering.scm (lepton-eda): Likewise.
(pcb): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/haskell.scm (ghc-7): Likewise.
* gnu/packages/irods.scm (irods): Likewise.
* gnu/packages/language.scm (python2-tegaki-pygtk): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-lzlib): Likewise.
(sbcl-cl-gobject-introspection): Likewise.
(sbcl-cl-ana): Likewise.
(sbcl-cl-libuv): Likewise.
(sbcl-cl-async): Likewise.
(sbcl-mcclim): Likewise.
(sbcl-zstd): Likewise.
(sbcl-cl-opengl): Likewise.
(sbcl-lev): Likewise.
(sbcl-cl-glfw3): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
* gnu/packages/messaging.scm (utox): Likewise.
* gnu/packages/mpi.scm (java-openmpi): Likewise.
* gnu/packages/music.scm (jack-select): Likewise.
* gnu/packages/pascal.scm (fpc): Likewise.
* gnu/packages/python-crypto.scm (python-libnacl): Likewise.
* gnu/packages/python-xyz.scm (python-cairocffi): Likewise.
(python-pyev): Likewise.
(python-pytidylib): Likewise.
* gnu/packages/radio.scm (unixcw): Likewise.
* gnu/packages/rust.scm (rust-1.32): Likewise.
* gnu/packages/security-token.scm (opensc): Likewise.
(python-pyscard): Likewise.
* gnu/packages/selinux.scm (python-setools): Likewise.
* gnu/packages/spice.scm (libcacard): Likewise.
* gnu/packages/telephony.scm (libtgvoip): Likewise.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès
425ccde6ae
gnu: Use 'search-input-directory' when looking for C/C++ library headers. 
* gnu/packages/arcan.scm (arcan)[arguments]: Use
'search-input-directory' for "include/libdrm" and "include/apr-1".
* gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish.
* gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers.
* gnu/packages/cedille.scm (cedille): Likewise for IAL headers.
* gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx
headers.
* gnu/packages/cups.scm (hplip): Likewise for libusb headers.
* gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers.
* gnu/packages/game-development.scm (python2-renpy): Likewise for
fribidi headers.
* gnu/packages/games.scm (pokerth): Likewise for libircclient.
* gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile.
* gnu/packages/hurd.scm (hurd): Likewise for libtirpc.
* gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for
libcxx, catch2, and nlohmann-json-cpp.
* gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's
errno.h.
* gnu/packages/kde-pim.scm (kdepim-runtime): Use
'search-input-directory' for "include/KF5".
(kmessagelib): Likewise.
* gnu/packages/kde.scm (kdeconnect): Likewise.
* gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc.
* gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband".
* gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h"
and "aspell.h".
* gnu/packages/radio.scm (dream): Use 'search-input-file' and
'search-input-directory' for pulseaudio, sndfile, etc.
* gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and
libaudit.
* gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for
libcxx.
* gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5".
* gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest".
(libopenshot): Likewise for "include/UnitTest++".
* gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for
protobuf file.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès
1ec13efbd2
gnu: Use 'search-input-directory' for the Eigen header directory. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-directory' when searching for Eigen headers.
* gnu/packages/bioinformatics.scm (nanopolish): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
 2021-07-24 16:23:22 +02:00
Ludovic Courtès
6ea7297ea4
gnu: Use 'search-input-directory' when looking for tzdata. 
* gnu/packages/backup.scm (duplicity)[arguments]: Use
'search-input-directory' for "share/zoneinfo".
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Likewise.
(pigx-bsseq): Likewise.
* gnu/packages/calcurse.scm (calcurse): Likewise.
* gnu/packages/calendar.scm (date): Likewise.
* gnu/packages/compression.scm (lhasa): Likewise.
* gnu/packages/cran.scm (r-rstan): Likewise.
* gnu/packages/django.scm (python-django): Likewise.
* gnu/packages/dlang.scm (ldc-bootstrap): Likewise.
* gnu/packages/finance.scm (ledger): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/kde-frameworks.scm (kcalendarcore): Likewise.
(kdelibs4support): Likewise.
* gnu/packages/kodi.scm (kodi): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/perl.scm (perl-libtime-parsedate): Likewise.
* gnu/packages/python-xyz.scm (python-robotframework): Likewise.
(python-dparse): Likewise.
* gnu/packages/rrdtool.scm (rrdtool): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/vim.scm (vim): Likewise.
* gnu/packages/virtualization.scm (ganeti): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
* gnu/packages/xfce.scm (xfce4-panel): Likewise.
* gnu/packages/mate.scm (libmateweather): Use 'search-input-file' for
"share/zoneinfo/zone.tab".
 2021-07-24 16:23:22 +02:00
Efraim Flashner
fd8aea010f
gnu: python-pysam: Make the check phase honor the tests? argument. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
 2021-07-22 10:58:22 +03:00
Efraim Flashner
877792a6a7
gnu: python-pysam: Update to 0.16.0.1. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
 2021-07-22 10:57:41 +03:00
Efraim Flashner
cc4906d13b
gnu: Add htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
 2021-07-22 10:50:58 +03:00
Efraim Flashner
309b38bed6
gnu: python-biopython: Update to 1.73. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
 2021-07-22 09:14:12 +03:00
Lars-Dominik Braun
73830b5da3
gnu: Add r-battenberg. 
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
ed636babfa
gnu: Add r-ascat. 
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
690df95d1a
gnu: Add nanosv. 
* gnu/packages/bioinformatics.scm (nanosv): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
2b665b8a49
gnu: Add python-pyvcf. 
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
086c6800cf
gnu: checkm: Rename and update to 1.1.3. 
Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.

* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
18a02fe7ca
gnu: Add tombo. 
* gnu/packages/bioinformatics.scm (tombo): New variable.
 2021-07-21 13:36:07 +02:00
Ludovic Courtès
0e47fcced4
Merge branch 'master' into core-updates 2021-07-18 19:50:01 +02:00
Julien Lepiller
ef79d6c5d6
gnu: Add ocaml-sqlite3. 
* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
(ocaml4.07-sqlite3): Inherit from ocaml-sqlite3.
* gnu/packages/bioinformatics.scm (pplacer): Also use package-with-ocaml4.07
with ocaml-sqlite3.
 2021-07-05 16:54:11 +02:00
Ludovic Courtès
ebb8e44a4a
gnu: bioperl-minimal: Avoid top-level cross-module references. 
This could lead to circular reference breakage.

* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
 2021-07-01 17:13:13 +02:00
Ludovic Courtès
b17ee44212
gnu: Do not import (gnu packages commencement). 
Line introduced in 4efbf56e53.

* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
 2021-07-01 17:13:13 +02:00
Tobias Geerinckx-Rice
9dea3f101f
Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/cups.scm
	gnu/packages/python-web.scm
	gnu/packages/web.scm
	guix/build/maven/pom.scm
 2021-06-23 18:45:21 +02:00
Efraim Flashner
07d2c72d39
gnu: ensembl-vep: Use a source file-name. 
* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
 2021-06-22 13:49:05 +03:00
Ricardo Wurmus
44bccf414b
gnu: Add perl-cworld-dekker. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
 2021-06-22 08:40:56 +02:00
Ricardo Wurmus
8a62d8685a
gnu: Add python-iced. 
* gnu/packages/bioinformatics.scm (python-iced): New variable.
 2021-06-21 13:02:39 +02:00
Marius Bakke
6f9a80b331
Merge branch 'master' into core-updates 
Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a277 and
12964df69a respectively.

4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.

 Conflicts:
	gnu/local.mk
	gnu/packages/aidc.scm
	gnu/packages/boost.scm
	gnu/packages/curl.scm
	gnu/packages/nettle.scm
	gnu/packages/networking.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tls.scm
 2021-06-19 17:38:47 +02:00
Ricardo Wurmus
748d3a2b8a
gnu: Add python-cgatcore. 
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
 2021-06-14 23:13:56 +02:00
Maxim Cournoyer
ea0a51071e
gnu: Rename qtbase to qtbase-5. 
This change was automated via the following command:

$ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g'
$ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g'
$ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g'
$ git checkout etc    # to clear some spurious changes

This is done so the qtbase package can be upgraded to version 6 in the
following commit.
 2021-06-14 00:24:42 -04:00
Ricardo Wurmus
ac51eb1125
gnu: pigx-sars-cov2-ww: Update to 0.0.2. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
 2021-06-08 22:43:47 +02:00
Ricardo Wurmus
c9e8e7b0bf
gnu: pigx-bsseq: Update to 0.1.5. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
 2021-06-08 16:35:17 +02:00
Mădălin Ionel Patrașcu
dd3698c1ac
gnu: python-hicmatrix: Update to 15. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-06-08 16:35:17 +02:00
Efraim Flashner
61bce4d143
gnu: python-mappy: Move to (gnu packages bioinformatics). 
* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
 2021-06-08 09:50:55 +03:00
Ricardo Wurmus
4a01e00a13
gnu: pigx-rnaseq: Update to 0.0.17. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
 2021-06-08 00:53:06 +02:00
Ricardo Wurmus
be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus
bb38287570
gnu: salmon: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus
9875dae429
gnu: macs: Update to 2.2.7.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus
1ace395f9c
gnu: libgff: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus
176513f5f3
gnu: jellyfish: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus
1ac8f05103
gnu: multiqc: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
 2021-06-07 10:53:16 +02:00
Mădălin Ionel Patrașcu
a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3. 
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Marius Bakke
8d59c262ad
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/algebra.scm
	gnu/packages/bioinformatics.scm
	gnu/packages/curl.scm
	gnu/packages/docbook.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/maths.scm
	gnu/packages/plotutils.scm
	gnu/packages/python-web.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/readline.scm
	gnu/packages/tls.scm
	gnu/packages/xml.scm
	gnu/packages/xorg.scm
 2021-06-06 21:16:32 +02:00
Efraim Flashner
b65c02e2d3
gnu: freebayes: Update to 1.3.5. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-06-06 12:13:28 +03:00
Mădălin Ionel Patrașcu
d1e7b50dbf
gnu: python-cooler: Update to 0.8.11. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
 2021-06-06 08:33:21 +02:00
Ricardo Wurmus
f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
 2021-06-05 09:12:39 +02:00
Roel Janssen
7382aa00b8
gnu: python-scanpy: Update to 1.7.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
 2021-06-04 23:51:35 +02:00
Maxime Devos
b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (nanopolish)[arguments]<#:phases>{wrap-programs}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:33 +02:00
Maxime Devos
2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (gess)[arguments]<#:phases>{install}
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:32 +02:00
Maxime Devos
c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (prinseq)[arguments]<#:phases>{install}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:32 +02:00
Maxime Devos
fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (proteinortho)[arguments]<#:phases>{wrap-programs}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:32 +02:00
Ricardo Wurmus
d06ae05808
gnu: Add pigx-sars-cov2-ww. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
 2021-06-04 12:57:08 +02:00
Ricardo Wurmus
0928e55266
gnu: Add fit-sne. 
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
 2021-06-03 12:22:29 +02:00
Ricardo Wurmus
011d586c2c
gnu: Add biobambam2. 
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
 2021-06-02 13:54:15 +02:00
Ricardo Wurmus
18e0081045
gnu: Add libmaus2. 
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
 2021-06-02 13:54:15 +02:00
Roel Janssen
7ae2b1f2dc
gnu: Add bamutils. 
* gnu/packages/bioinformatics.scm (bamutils): New variable.
 2021-06-01 13:14:38 +02:00
Ricardo Wurmus
f463f376e9
gnu: bits: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:10:20 +02:00