68619cad28
gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2.
...
* gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to
1.1.2.
[arguments]: Override; delete 'sanity-check phase.
[propagated-inputs]: Override and add python2-six.
(python-sphinxcontrib-websupport)[properties]: Record python2-variant.
2021-12-08 16:13:08 +01:00
a4a7c78f68
gnu: python2-jinja2: Downgrade to 2.11.3
...
* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version
supporting Python 2.
(python-jinja2)[properties]: Record python2-variant.
2021-12-08 16:13:08 +01:00
14ed9b049e
gnu: python2-markupsafe: Downgrade to 1.1.1.
...
* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1,
because that's the last version to support Python 2.
2021-12-08 14:43:38 +01:00
c8060055de
gnu: ocaml-mcl: Add -fcommon to compiler flags.
...
* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon.
2021-12-08 14:31:54 +01:00
b835d10d61
gnu: paml: Pass -fcommon to compiler.
...
* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
2021-12-08 14:31:54 +01:00
2157d82ed3
gnu: paml: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from
build phases.
2021-12-08 14:31:54 +01:00
76b39f03d2
gnu: sambamba: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T
from build phases.
2021-12-08 14:31:54 +01:00
62da1b34d1
gnu: discrover: Add texlive-fonts-ec to inputs.
...
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-fonts-ec.
2021-12-08 14:31:54 +01:00
62e196608c
gnu: discrover: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T
from build phases.
2021-12-08 14:31:54 +01:00
1f63c46a1c
gnu: tbsp: Update to 1.0.0-2.dc30c03.
...
* gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03.
[arguments]: Relax requirement on matplot. This may turn out to be a mistake.
[inputs]: Replace python-biopython with python-biopython-1.73.
2021-12-08 14:31:54 +01:00
1f7c06965c
gnu: mantis: Update to 0.1-2.b6979a2.
...
* gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2.
[arguments]: Disable the use of SSE4.2 instructions.
[native-inputs]: Build with GCC 7.
2021-12-08 14:31:53 +01:00
738f22fa06
gnu: imp: Disable tests.
...
* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test
suite.
2021-12-08 14:31:53 +01:00
acfbb53222
gnu: snap-aligner: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
2021-12-08 14:31:53 +01:00
42a7b5215b
gnu: snap-aligner: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T
from 'install phase.
2021-12-08 14:31:53 +01:00
7c58677a29
gnu: snap-aligner: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS?
option.
2021-12-08 14:31:53 +01:00
298a8d0b89
gnu: khmer: Cythonize source files.
...
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files.
[arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp
files from Cython sources; add 'build-extensions phase; replace 'check phase.
2021-12-08 14:31:53 +01:00
9a19e8f609
gnu: cwltool: Update to 3.1.20211107152837.
...
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837.
[arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T
from build phases; fix /bin/sh invocations in test files.
2021-12-08 14:31:52 +01:00
ee03b51f6e
gnu: lollypop: Build with libsoup@2.
...
* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to
LIBSOUP-MINIMAL-2.
2021-12-08 08:45:11 +01:00
637735da4d
gnu: rhythmbox: Adjust inputs.
...
* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to
PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
2021-12-08 08:45:11 +01:00
14bc2ce43a
gnu: labelme: Loosen Python requirements.
...
* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it
does not require a specific version of Matplotlib.
2021-12-08 08:45:11 +01:00
5fb1ba880f
gnu: newick-utils: Pass -fcommon to compiler.
...
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
2021-12-07 23:27:40 +01:00
ed5e6c7502
gnu: blasr: Update to 5.3.5.
...
* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
2021-12-07 23:20:36 +01:00
38cf62a236
gnu: blasr: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from
build phase.
2021-12-07 23:20:36 +01:00
d068de0c7d
gnu: blasr-libcpp: Update to 5.3.5.
...
* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5.
[inputs]: Add htslib.
2021-12-07 23:20:36 +01:00
b81daed2de
gnu: htseq: Update to 0.12.3.
...
* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
2021-12-07 23:20:36 +01:00
6eecbfb9ac
gnu: clipper: Update to 2.0.1.
...
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1.
[source]: Add snippet to remove pre-compiled files.
[arguments]: Disable tests, delete 'sanity-check phase, and add
'use-python3-for-cython phase.
2021-12-07 23:20:36 +01:00
fc797a3e8f
gnu: pbbam: Update to 1.7.0.
...
* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
2021-12-07 23:20:30 +01:00
b764d10e91
gnu: bwa-pssm: Fix build.
...
* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase
'patch-C-error.
2021-12-07 17:53:14 +01:00
4195a877cb
gnu: Add pbcopper.
...
* gnu/packages/bioinformatics.scm (pbcopper): New variable.
2021-12-07 16:00:22 +01:00
8dcf062f28
gnu: python-ndg-httpsclient: Add missing input.
...
* gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add
python-pyasn1.
2021-12-07 15:39:18 +01:00
a98fe1d46e
gnu: fsom: Build with GCC 6.
...
* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6.
[arguments]: Remove trailing #T.
2021-12-07 15:37:16 +01:00
cbef1824da
gnu: python-velocyto: Remove generated C files.
...
* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all
generated .c files.
2021-12-07 15:31:33 +01:00
6e67cda755
gnu: python-schema-salad: Update to 8.2.20211116214159.
...
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
8.2.20211116214159.
[arguments]: Remove trailing #T.
[propagated-inputs]: Replace python-cachecontrol-0.11 with
python-cachecontrol.
[native-inputs]: Add python-black.
2021-12-07 15:28:13 +01:00
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
00ba04020e
gnu: taxtastic: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
2021-12-07 15:12:15 +01:00
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
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
92a2f55cf9
gnu: Add python-cytoolz-for-cooler.
...
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
2021-12-07 13:24:49 +01:00
c08d6e63a0
gnu: python-sparse: Update to 0.13.0.
...
* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
2021-12-07 13:16:47 +01:00
224d1c5818
gnu: python-dask: Update to 2021.11.2.
...
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2.
[source]: Fetch from github.
[arguments]: Remove phase 'disable-broken-tests.
2021-12-07 13:07:46 +01:00
ed15986a32
gnu: python-dask: Run tests conditionally.
...
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
2021-12-07 13:07:23 +01:00
ad17046040
gnu: python-dask: Add missing input for tests.
...
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add
python-pytest-rerunfailures.
2021-12-07 13:06:37 +01:00
899121f4d6
gnu: phylip: Update to 3.697.
...
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
2021-12-07 13:05:53 +01:00
e86fe9801e
gnu: phylip: Pass -fcommon to compiler.
...
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
2021-12-07 13:05:35 +01:00
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
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
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
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
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
417299f004
gnu: python-pytest-console-scripts: Update to 1.2.1.
...
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to
1.2.1.
2021-12-07 12:41:14 +01:00
Ricardo Wurmus
Marius Bakke