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
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
9dc727f827
gnu: hisat: Remove invalid characters.
...
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
2021-12-07 11:51:09 +01:00
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
b5c9afb7c5
gnu: Remove python2-bx-python.
...
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
2021-12-07 11:51:09 +01:00
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
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
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
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
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
1310879fb0
gnu: f-seq: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
2021-12-06 18:48:01 +01:00
9bc0f45df5
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-12-05 19:17:41 +01:00
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
dd67154e5d
gnu: Remove python2-plastid.
...
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
2021-12-05 17:37:05 +01:00
98264531be
gnu: Remove python2-twobitreader.
...
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
2021-12-05 17:36:43 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
db5646d957
gnu: Adjust for python-build-system behavior change.
...
Commit cb72f9a773
2021-12-05 14:02:10 +01:00
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
e70e26423b
gnu: minimap2: Update to 2.23.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
2021-12-05 11:51:10 +02:00
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
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
39e2a84f52
gnu: sailfish: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
2021-12-04 19:54:28 +01:00
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
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
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
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
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
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
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
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
8a446f5e41
gnu: preseq: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
2021-12-04 19:54:27 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
a6b6084649
gnu: mash: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04 00:30:44 +01:00
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
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
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04 00:19:08 +01:00
7c2ee27360
gnu: fastp: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04 00:16:10 +01:00
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
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
62e0641892
gnu: fxtract: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04 00:02:20 +01:00
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
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
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
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
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
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
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
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
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
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
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
d0aa14a43d
gnu: Add vbz-compression.
...
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
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
673cc29908
gnu: bamutils: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
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
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
b7aaf6c418
gnu: ivar: Disable parallel tests.
...
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
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
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
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
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
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
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
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
a8fff63daa
gnu: Add python-mygene.
...
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
2021-12-02 11:57:28 +01:00
b15a525703
gnu: Add python-biothings-client.
...
* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
2021-12-02 11:57:13 +01:00
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
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
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
Ricardo Wurmus
Marius Bakke
Efraim Flashner