Ricardo Wurmus
16474f85cf
gnu: taxtastic: Update to 0.9.2.
...
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust
'prepare-directory phase.
2021-12-07 15:13:06 +01:00
Ricardo Wurmus
00ba04020e
gnu: taxtastic: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
2021-12-07 15:12:15 +01:00
Ricardo Wurmus
58fecfd18e
gnu: python-dendropy: Update to 4.5.1.
...
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1.
[arguments]: Skip failing tests.
2021-12-07 14:53:37 +01:00
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
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
