0bcd28e58c
gnu: python-scanpy: Update to 1.9.1.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
2022-05-30 23:09:46 +02:00
cb115ba722
gnu: pigx-sars-cov-2: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
2022-05-29 00:39:19 +02:00
df3e5cfa05
gnu: pigx-bsseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
2022-05-29 00:34:29 +02:00
b64f4a1245
gnu: pigx-scrnaseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
2022-05-29 00:29:19 +02:00
add551f651
gnu: pigx-chipseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
2022-05-29 00:18:48 +02:00
b015a15c57
gnu: Fix all this damn packages.
...
* gnu/packages/bioinformatics.scm (r-icellnet)[description]:
Fix ‘this packages’ typo.
* gnu/packages/cran.scm (r-add2ggplot)[description]: Likewise.
* gnu/packages/crates-io.scm (rust-const-oid-0.6, rust-pem-rfc7468-0.2)
(rust-scrypt-0.8)[description]: Likewise.
2022-05-22 02:00:00 +02:00
dab819d5c4
Move (gnu platform) and (gnu platforms ...) to guix/.
...
* gnu/platform.scm:
* gnu/platforms/arm.scm:
* gnu/platforms/hurd.scm:
* gnu/platforms/mips.scm:
* gnu/platforms/powerpc.scm:
* gnu/platforms/riscv.scm:
* gnu/platforms/s390.scm:
* gnu/platforms/x86.scm: Move to guix/.
* Makefile.am:
* doc/guix.texi (Porting to a New Platform):
* etc/release-manifest.scm:
* gnu/ci.scm:
* gnu/image.scm:
* gnu/local.mk:
* gnu/packages/bioinformatics.scm:
* gnu/packages/bootstrap.scm:
* gnu/packages/cross-base.scm:
* gnu/packages/instrumentation.scm:
* gnu/packages/linux.scm:
* gnu/system/image.scm:
* gnu/system/images/hurd.scm:
* gnu/system/images/novena.scm:
* gnu/system/images/pine64.scm:
* gnu/system/images/pinebook-pro.scm:
* gnu/system/images/rock64.scm:
* guix/scripts/build.scm:
* guix/scripts/system.scm:
* guix/self.scm: Update (gnu platform...) to (guix platform...).
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-05-25 09:27:25 +02:00
b55310603f
linux: Remove system->linux-architecture procedure.
...
* gnu/packages/linux.scm (system->linux-architecture): Remove it.
(make-linux-libre-headers*, make-linux-libre*): Adapt them.
* guix/build-system/linux-module.scm (system->arch): Adapt it.
* gnu/packages/instrumentation.scm (uftrace): Ditto.
* gnu/packages/cross-base.scm (cross-kernel-headers): Ditto.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Ditto.
* doc/guix.texi (Porting to a new platform): Update it.
2022-05-22 15:15:33 +02:00
a1a55e5b60
gnu: fastahack: Wrap long line.
...
* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
2022-05-12 12:59:18 +05:30
aaa981f7c5
gnu: cwltool: Do not propagate inputs.
...
* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ...
[inputs]: ... here.
2022-05-11 10:52:45 +05:30
8d25887d87
gnu: vcflib: Set absolute path to pkg-config.
...
Setting the absolute path to pkg-config is required to support
cross-compilation.
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Set
PKG_CONFIG_EXECUTABLE in #:configure-flags.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:19:43 +03:00
9047a31152
gnu: vcflib: Find submodule sources in native-inputs during cross-compilation.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In the
unpack-submodule-sources phase, look for submodule sources in both inputs and
native-inputs.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:19:39 +03:00
9a68c07507
gnu: vcflib: Use G-expressions.
...
* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using
G-expressions.
[arguments]: Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:19:03 +03:00
9258576eea
gnu: fastahack: Use compiler specific to the build target.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Set CXX in
#:make-flags. In the build-dynamic phase, use cxx-for-target instead of g++.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:18:09 +03:00
713dadf47e
gnu: fastahack: Use G-expressions.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Rewrite
using G-expressions. Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:17:51 +03:00
086c7c143c
gnu: tabixpp: Fix cross-compilation.
...
tabixpp links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and
xz should be listed in inputs even though they are already present implicitly
in native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (tabixpp)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:17:25 +03:00
cbda00c499
gnu: tabixpp: Use build tools specific to the target.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Set CC and CXX in
#:make-flags. In the build-libraries phase, use cxx-for-target instead of g++
and ar-for-target instead of ar.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:15:12 +03:00
a990547952
gnu: tabixpp: Use #:make-flags.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Do not override the
build phase. Move the required make arguments to #:make-flags. Add
build-libraries phase.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:14:18 +03:00
ff1fd3b012
gnu: tabixpp: Use G-expressions.
...
* gnu/packages/bioinformatics.scm (tabixpp)[source]: Reindent.
[arguments]: Use search-input-file and search-input-directory.
[source, arguments]: Rewrite using G-expressions. Do not return #t from
snippets and custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:13:40 +03:00
6f5cbac67d
gnu: pigx-sars-cov-2: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
2022-05-06 15:34:31 +02:00
f550c0ccb0
gnu: Add pigx-sars-cov-2.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable.
(pigx-sars-cov2-ww): Deprecate this package in favor of the former.
2022-05-06 15:34:31 +02:00
39d6c13fda
gnu: python-hic2cool: Fix build.
...
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
2022-05-02 17:33:31 +02:00
b1dd32d8e3
gnu: htslib-for-stringtie: Inherit from htslib-1.12.
...
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
2022-05-02 14:35:26 +02:00
5caad9f252
gnu: python-cooler: Use more recent cytoolz.
...
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
2022-05-02 13:33:16 +02:00
33fe027f91
gnu: Add r-giotto.
...
* gnu/packages/bioinformatics.scm (r-giotto): New variable.
2022-04-26 09:48:14 +02:00
ffb616b69d
gnu: vcflib: Update to 1.0.3.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3.
[source]: Remove trailing #t.
[arguments]: Remove trailing #t from phases.
2022-04-19 21:56:50 +03:00
7034746e15
gnu: scregseg: Remove cythonized file.
...
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
2022-04-14 22:55:33 +03:00
c8a6e4abbc
gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).
...
* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
2022-04-14 13:35:22 +02:00
6413d0898b
gnu: Add r-copykat.
...
* gnu/packages/bioinformatics.scm (r-copykat): New variable.
2022-04-11 16:11:45 +02:00
96a132809f
gnu: smithwaterman: Fix cross-compiling.
...
The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences.
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More
closely match the 'ar' and 'ld' commands when substituting them.
2022-04-10 20:49:33 +03:00
e3e3381fdb
gnu: Add r-rnaseqdtu.
...
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-06 11:43:46 +02:00
df2dc0c416
gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.
...
This is needed since the update of python-loompy.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename
'set-PYTHONPATH to 'set-additional-environment-variables and set
NUMBA_CACHE_DIR.
2022-04-05 18:40:48 +02:00
e721122069
gnu: pigx-scrnaseq: Use new inputs style.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
2022-04-05 18:40:48 +02:00
5d1c9fcdcf
gnu: pigx-scrnaseq: Update to 1.1.8.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
[patches]: Remove.
[native-inputs]: Remove.
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-04-05 18:40:48 +02:00
345f79b2cf
gnu: freebayes: Fix test suite.
...
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
2022-04-04 22:58:25 +03:00
c1fc65ecb6
gnu: smithwaterman: Use new style for phases.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
2022-04-04 22:45:37 +03:00
855c8d9d41
gnu: smithwaterman: Fix cross-compiling.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add
make-flag to use cxx-for-target. Adjust custom 'patch-source and
'build-dynamic phases to use cross toolchain binaries when cross
compiling. Remove trailing #t from phases.
2022-04-04 22:41:54 +03:00
05e68f31ba
gnu: python-velocyto: Set cache directory for Numba.
...
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
2022-03-31 16:02:21 +02:00
8f3dc994bb
gnu: wfmash: Enable test suite.
...
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
2022-03-31 16:29:34 +03:00
1ca9d9e194
gnu: Add wfmash.
...
* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:53 +03:00
7d331dd203
gnu: htslib: Add bzip2 and xz to inputs.
...
htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:52 +03:00
a69a44bf59
gnu: python-loompy: Update to 3.0.7.
...
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
2022-03-31 14:37:58 +02:00
591007f7d1
gnu: r-signac: Update to 1.6.0-2.458e647.
...
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 17:40:17 +02:00
977a33139e
gnu: plink-ng: Update to 2.00a3-20220315.
...
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
2022-03-29 15:33:55 +02:00
d710f01957
gnu: Add r-cytobackbone.
...
* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 14:03:44 +02:00
6d5964e804
gnu: pigx-sars-cov2-ww: Update to 0.0.5.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
847acc3206
gnu: pigx-rnaseq: Update to 0.0.20.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
a9429c8f22
Merge branch 'staging' into core-updates.
2022-03-21 23:39:43 -04:00
ca588fdfde
gnu: Add r-scopeloomr.
...
* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
2022-03-09 11:35:59 +01:00
e5dbda5abc
gnu: texlive-latex-pgf: Rename to "texlive-pgf".
...
Suggested by Ricardo Wurmus.
* gnu/packages/tex.scm (texlive-latex-pgf): Rename to...
(texlive-pgf): ... this. Change 'name' accordingly.
(texlive-latex-pgf): Define as deprecated.
(texlive-beamer)[propagated-inputs]: Use the new name.
(texlive-todonotes)[propagated-inputs]: Likewise.
(texlive-adjustbox)[propagated-inputs]: Likewise.
(texlive-tcolorbox)[propagated-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
2022-03-02 19:26:16 +01:00
a6867b2d98
gnu: minimap2: Update to 2.24.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
2022-02-27 11:42:30 +02:00
3fb78caa55
gnu: Add r-dyngen.
...
* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
2022-02-22 18:48:30 +01:00
d293162615
gnu: Add texlive-pgf.
...
* gnu/packages/tex.scm (texlive-pgf): New variable.
(texlive-latex-pgf): Deprecate variable.
(texlive-beamer):
(texlive-latex-xkeyval):
(texlive-todonotes):
(texlive-adjustbox):
(texlive-tcolorbox):
* gnu/packages/bioinformatics.scm (discrover): Use new variable.
2022-02-14 00:08:30 +01:00
970b7a949d
gnu: Add texlive-graphics.
...
* gnu/packages/tex.scm (texlive-graphics): New variable.
(texlive-latex-graphics): Deprecate variable.
(texlive-base):
(texlive-pstool):
(texlive-jadetex):
* gnu/packages/bioinformatics.scm (velvet):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-numpy-documentation):
(python-ipython-documentation):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/statistics.scm (r-with-tests): Use new variable.
2022-02-14 00:08:30 +01:00
94268d5021
gnu: Add texlive-ms.
...
* gnu/packages/tex.scm (texlive-ms): New variable.
(texlive-latex-ms): Deprecate variable.
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/python-xyz.scm (python-nbconvert): Use new variable.
2022-02-14 00:08:29 +01:00
b5d472ef5d
gnu: python-gffutils: Update to 0.10.1.
...
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1.
[arguments]: Remove obsolete phase. Respect TESTS? in check phase while at
it.
2022-02-15 00:21:16 +01:00
7fc8a6faf6
gnu: Add scvelo.
...
* gnu/packages/bioinformatics.scm (scvelo): New variable.
2022-01-31 16:07:40 +01:00
cd4bf5ecb4
gnu: python-louvain-0.6: Update to 0.7.1.
...
* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1.
[arguments]: Add build phases 'find-igraph and 'pretend-version.
[native-inputs]: Add python-setuptools-scm and python-wheel.
Rename this variable...
(python-louvain-0.7): ...to this, naturally.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update
reference to python-louvain-0.6.
2022-01-31 16:07:39 +01:00
9ce1fd24e3
gnu: bwa-meth: Remove trailing #T from build phase.
...
* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
2022-01-31 16:07:39 +01:00
f32a49fceb
gnu: bwa-meth: Update to 0.2.3.
...
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
2022-01-31 16:07:39 +01:00
f00ed43653
gnu: pigx-sars-cov2-ww: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set
PYTHONPATH variable in new build phase.
2022-01-27 22:15:25 +01:00
aa649ae231
gnu: pigx-scrnaseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
f4cbf11c65
gnu: pigx-bsseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
f127bce3ec
gnu: pigx-chipseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
c6bf89cff0
gnu: pigx-rnaseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
ed9ca97409
gnu: cwltool: Update to 3.1.20220119140128.
...
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20220119140128.
[propagated-inputs]: Change from PYTHON-RDFLIB-5 to PYTHON-RDFLIB.
[native-inputs]: Remove PYTHON-RDFLIB-JSONLD.
2022-01-22 10:23:01 +01:00
af473726b2
gnu: python-pyvcf: Build with old setuptools.
...
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add
PYTHON-SETUPTOOLS.
2022-01-22 10:23:01 +01:00
ce291b193c
gnu: Add r-scseqcomm.
...
* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
2022-01-21 15:53:18 +01:00
dac6b53c7e
gnu: Add r-icellnet.
...
* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
2022-01-21 15:53:18 +01:00
d99e42d7f6
gnu: samtools-0.1: Install headers and library.
...
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases
'install-library and 'install-headers.
2022-01-20 15:25:56 +01:00
61d7da5a1f
gnu: Add r-doubletfinder.
...
* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
2022-01-20 12:00:03 +01:00
2a4c271e61
gnu: python-rdflib: Update to 6.1.1.
...
* gnu/packages/rdf.scm (python-rdflib): Update to 6.1.1.
[arguments]: Remove #:tests. Add #:phases.
[native-inputs]: Change from PYTHON-NOSE to PYTHON-PYTEST.
(python-rdflib-5): New variable.
(python2-rdflib): Inherit from PYTHON-RDFLIB-5.
* gnu/packages/python-xyz.scm (python-prov): Change from PYTHON-RDFLIB to
PYTHON-RDFLIB-5.
* gnu/packages/bioinformatics.scm (cwltool): Likewise.
2022-01-18 19:35:55 +01:00
276f40fdc3
Merge branch 'version-1.4.0'
...
With resolved conflicts in:
gnu/packages/gnome.scm
gnu/packages/openstack.scm
gnu/packages/python-xyz.scm
2022-01-17 11:47:09 -05:00
4acf325150
gnu: sambamba: Update to 0.8.2.
...
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.2.
[arguments]: Sett CC and D_LD in build phase.
[native-inputs]: Add ld-gold-wrapper and binutils-gold.
2022-01-17 08:32:44 +01:00
b9e703da9d
gnu: clipper: Remove obsolete phase.
...
* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove
'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10 11:44:48 -05:00
85e43978a4
gnu: python-biom-format: Remove obsolete phase.
...
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]
<#:phases>: Remove 'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10 11:44:47 -05:00
64dac22b17
gnu: python-pysam: Update to 0.18.0.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0.
[source]: Add FIXME to clarify bundled libraries in use.
[phases]{check}: Streamline.
[propagated-inputs]: Use latest htslib (1.14).
[native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
2022-01-10 11:44:46 -05:00
801d0ed622
gnu: bcftools: Update to 1.14.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14.
(bcftools-1.12): New variable.
(bcftools-1.10): Use package/inherit and delete trailing #t.
[name]: Delete field.
2022-01-10 11:44:46 -05:00
23fdb5a69c
gnu: samtools: Update to 1.14.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14.
[modules]: Delete argument.
[phases]{install-library, install-headers}: Delete phases. This version no
longer includes the legacy library (it links to htslib directly).
(samtools-1.12): New variable.
2022-01-10 11:44:46 -05:00
74af2dd148
gnu: htslib: Update to 1.14.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.14.
(htslib-1.12): New variable.
(htslib-1.10, htslib-1.9, htslib-1.3)
(htslib-for-samtools-1.2): Normalize style.
2022-01-10 11:44:46 -05:00
946fd9be16
gnu: stringtie: Update to 2.2.0.
...
* gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0.
[source]: Simplify snippet.
[arguments]: Add make-flags; update build phases.
[inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and
libdeflate.
[license]: Change to Expat license.
2022-01-11 14:19:54 +01:00
9966f98b1b
gnu: Add htslib-for-stringtie.
...
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): New variable.
* gnu/packages/patches/htslib-for-stringtie.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2022-01-11 14:19:53 +01:00
603dd56be1
gnu: r-archr: Update to 1.0.1-1.92ab814.
...
* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814.
2022-01-04 16:08:03 +01:00
38376090c3
gnu: Remove trailing period from synopsis.
...
* gnu/packages/anddroid.scm (android-liblog, git-repo)[synopsis]: Remove
trailing period.
* gnu/packages/audio.scm (audio-to-midi)[synopsis]: Likewise.
* gnu/packages/bioinformatics.scm (python-mygene, python-scanpy,
nanosv)[synopsis]: Likewise.
* gnu/packages/cran.scm (r-gsubfn)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-ascii-1, rust-bindgen-0.59,
rust-byte-unit-4, rust-clircle-0.3, rust-dashmap-4, rust-dhcp4r-0.2,
rust-fast-float-0.2, rust-fst-0.4, rust-futures-core-preview-0.3,
rust-http-types-2, rust-hyper-0.14, rust-indexmap-1,
rust-minimal-lexical-0.1, rust-oorandom-11.1, rust-runtime-raw-0.3,
rust-sharded-slab-0.1, rust-takeable-option-0.4, rust-tower-service-0.3,
rust-ttf-parser-0.12)[synopsis]: Likewise.
* gnu/packages/disk.scm (f3)[synopsis]: Likewise.
* gnu/packages/emacs-xyz.scm (emacs-scribble-mode, emacs-psession)[synopsis]:
Likewise.
* gnu/packages/golang.scm (go-github-com-kylelemons-godebug)[synopsis]:
Likewise.
* gnu/packages/haskell-xyz.scm (ghc-fsnotify, ghc-libyaml, ghc-emojis,
ghc-regex-tdfa, ghc-th-lift-instances, ghc-commonmark-pandoc)[synopsis]:
Likewise.
* gnu/packages/java.scm (java-commons-jxpath, java-jakarta-regexp)[synopsis]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-cl-annot, sbcl-envy)[synopsis]: Likewise.
* gnu/packages/mail.scm (go-gitlab.com-shackra-goimapnotify)[synopsis]:
Likewise.
* gnu/packages/maven.scm (maven-wagon-http-shared,
maven-surefire-plugin)[synopsis]: Likewise.
* gnu/packages/perl.scm (perl-text-soundex)[synopsis]: Likewise.
* gnu/packages/python-check.scm (python-httmock)[synopsis]: Likewise.
* gnu/packages/python-web.scm (python-bottle)[synopsis]: Likewise.
* gnu/packages/python-xyz.scm (python-olefile, python-tokenize-rt,
python-pylzma)[synopsis]: Likewise.
* gnu/packages/tex.scm (texlive-docstrip)[synopsis]: Likewise.
2021-12-30 19:11:46 -08:00
95ec0ae948
gnu: python-pyspoa: Fix trailing whitespace in synopsis.
...
* gnu/packages/bioinformatics.scm (python-pyspoa)[synopsis]: Fix trailing
whitespace.
2021-12-30 00:50:41 -08:00
97eb82fdb2
gnu: lofreq: Fix trailing whitespace in synopsis.
...
* gnu/packages/bioinformatics.scm (lofreq)[synopsis]: Fix trailing whitespace.
2021-12-30 00:50:36 -08:00
3c44bd85e3
gnu: arriba: Fix trailing whitespace in synopsis.
...
* gnu/packages/bioinformatics.scm (arriba)[synopsis]: Fix trailing whitespace.
2021-12-30 00:50:31 -08:00
70ddfa230d
gnu: ivar: Fix trailing whitespace in description.
...
* gnu/packages/bioinformatics.scm (ivar)[description]: Fix trailing
whitespace.
2021-12-29 22:47:28 -08:00
62d2c36e77
gnu: sortmerna: Update to 4.3.4.
...
* gnu/packages/bioinformatics.scm (sortmerna): Update to 4.3.4.
[build-system]: Use cmake-build-system.
[arguments]: Disable tests; add configure flags; add phase
'find-concurrentqueue-headers; update 'install phase.
[inputs]: Add concurrentqueue, gflags, rapidjson, and rocksdb.
[native-inputs]: Add pkg-config.
2021-12-20 23:23:40 +01:00
e661f4eff4
gnu: Remove unneeded uses of custom GCC versions.
...
* gnu/packages/bioinformatics.scm (libmaus2, biobambam2)[native-inputs]:
Remove GCC-10.
* gnu/packages/game-development.scm (libresprite, python-pyxel)[native-inputs]: Likewise.
* gnu/packages/lua.scm (emilua)[native-inputs]: Likewise.
* gnu/packages/radio.scm (sdr++)[native-inputs]: Likewise.
* gnu/packages/wm.scm (fnott)[native-inputs]: Likewise.
* gnu/packages/text-editors.scm (kakoune)[native-inputs]: Likewise.
(scintilla)[native-inputs]: Remove GCC-9.
* gnu/packages/build-tools.scm (bear)[native-inputs]: Likewise.
* gnu/packages/cpp.scm (magic-enum)[native-inputs]: Likewise.
* gnu/packages/games.scm (openttd)[native-inputs]: Likewise.
(schiffbruch)[native-inputs]: Remove GCC-11.
* gnu/packages/music.scm (liquidsfz, geonkick)[native-inputs]: Remove GCC-9.
* gnu/packages/fcitx5.scm (fcitx5, libime, fcitx5-configtool)[native-inputs]:
Likewise.
* gnu/packages/wine.scm (dxvk32)[native-inputs]: Likewise.
* gnu/packages/ftp.scm (libfilezilla)[native-inputs]: Remove GCC-8.
* gnu/packages/image.scm (blurhash)[native-inputs]: Likewise.
* gnu/packages/jami.scm (libring)[native-inputs]: Likewise.
* gnu/packages/pdf.scm (xournalpp)[native-inputs]: Likewise.
* gnu/packages/telegram.scm (webrtc-for-telegram-desktop,
telegram-desktop)[native-inputs]: Likewise.
2021-12-17 19:07:17 +01:00
8394619bac
gnu: Simplify package inputs.
...
This commit was obtained by running:
./pre-inst-env guix style
without any additional argument.
2021-12-13 17:48:25 +01:00
4992858e21
gnu: salmon: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (salmon): Update to 1.6.0.
[inputs]: Update pufferfish sources.
2021-12-12 12:41:54 +01:00
32750e8c3e
Merge remote-tracking branch 'signed/master' into core-updates
2021-12-10 21:49:25 +01:00
af5fa4d202
gnu: Add ccwl.
...
* gnu/packages/bioinformatics.scm (ccwl): New variable.
2021-12-10 15:26:59 +05:30
77ea796d1b
gnu: pplacer: Fix build.
...
* gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with
gsl-static.
* gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same.
2021-12-09 23:17:26 +02:00
1e81140cb5
gnu: python-dendropy: Skip additional test.
...
* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust
custom 'skip-broken-tests phase to skip additional test.
2021-12-09 22:43:42 +02:00
f0cc0e8f30
gnu: imp: Build with default cmake.
...
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
2021-12-09 14:39:22 +02:00
2648d3207f
gnu: repeat-masker: Update to 4.1.2-p1.
...
* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.
2021-12-09 12:10:18 +01:00
0bf3c9abaa
gnu: metabat: Update to 2.15.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 2.15.
[source]: Remove patch.
[build-system]: Use cmake-build-system.
[arguments]: Adjust to new build system.
* gnu/packages/patches/metabat-fix-compilation.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-12-09 11:50:10 +01:00
1c7914009a
gnu: seek: Update to 1-1.196ed4c.
...
* gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c.
[source]: Fetch from github.
[build-system]: Use cmake-build-system.
[arguments]: Remove all custom phases; replace 'check phase; disable tests;
set configure flags.
[inputs]: Add apache-thrift:include, apache-thrift:lib, and python.
[native-inputs]: Remove autoconf, automake, and perl; add pkg-config.
2021-12-09 11:17:45 +01:00
26e26bc819
gnu: miso: Update to 0.5.4-1.b714021.
...
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021.
[source]: Fetch via git; simplify snippet.
[inputs]: Replace samtools with samtools-1.2.
[home-page]: Update to new location.
2021-12-09 11:17:45 +01:00
0b8a75cc3a
gnu: Add samtools-1.2.
...
* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
2021-12-09 11:17:45 +01:00
f505f588a7
gnu: Add htslib-for-samtools-1.2.
...
* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
2021-12-09 11:17:45 +01:00
00ae87c41a
gnu: tadbit: Update to 1.0.1-1.5c4c1dd.
...
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd.
[arguments]: Remove trailing #T from build phases; pass -fcommon to test
binaries; run tests conditionally.
2021-12-08 16:32:37 +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
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
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
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
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
b15e543d30
Merge branch 'master' into core-updates-frozen
2021-11-23 11:29:38 +01:00
e74bcbc64f
gnu: python-scanpy: Set PYTHONPATH variable.
...
This is a follow-up to commit 664721422c
2021-11-21 09:07:50 +01:00
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
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
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
55870e86d9
gnu: multiqc: Remove sanity check.
...
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
2021-11-21 00:39:09 +01:00
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
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
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
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
3a317f7476
Merge branch 'master' into core-updates-frozen
2021-11-17 23:43:14 +01:00
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
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
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
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
6be47c5bc5
gnu: Add circtools.
...
* gnu/packages/bioinformatics.scm (circtools): New variable.
2021-11-11 15:39:19 +00:00
b8c9f061e1
gnu: Add bioparser.
...
* gnu/packages/bioinformatics.scm (bioparser): New variable.
2021-11-11 15:39:19 +00:00
4052310e91
gnu: Add biosoup.
...
* gnu/packages/bioinformatics.scm (biosoup): New variable.
2021-11-11 15:39:19 +00:00
1c94392a13
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-11-08 09:06:14 +02:00
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
bc5155b952
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-10-31 14:49:47 +02:00
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
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
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
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
da526f33f2
gnu: cutadapt: Regenerate Cython files.
...
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
2021-10-24 21:23:20 +00:00
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
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
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
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
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
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
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
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
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
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
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
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
973b21aa6a
gnu: Add r-umi4cpackage.
...
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
2021-10-24 13:45:46 +00:00
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
4a0cd6297a
gnu: Add qtltools.
...
* gnu/packages/bioinformatics.scm (qtltools): New variable.
2021-10-22 21:29:25 +00:00
a8bac123f0
gnu: Add gdc-client.
...
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
2021-10-21 14:49:01 +00:00
f65917f607
gnu: Add r-shaman.
...
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
2021-10-21 14:34:35 +00:00
4885f40b80
gnu: Add r-misha.
...
* gnu/packages/bioinformatics.scm (r-misha): New variable.
2021-10-21 14:25:44 +00:00
42c9b75b25
gnu: Add ciri-long.
...
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
2021-10-21 13:39:36 +00:00
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
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
57841a91f5
gnu: Add python-bwapy.
...
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
2021-10-21 12:23:25 +00:00
6526c35df5
gnu: Add python-pyspoa.
...
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
2021-10-21 12:23:22 +00:00
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
a1eca979fb
Merge remote-tracking branch 'origin/master' into core-updates-frozen.
2021-10-12 17:46:23 +00:00
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
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
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
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
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
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
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
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
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
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
f80824fe09
gnu: Add r-presto.
...
* gnu/packages/bioinformatics.scm (r-presto): New variable.
2021-09-20 17:23:16 +02:00
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
d9dfbf886d
Merge branch 'master' into core-updates-frozen
2021-09-07 14:19:08 +02:00
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
c82b723bf8
gnu: Add megadepth.
...
* gnu/packages/bioinformatics.scm (megadepth): New variable.
2021-09-06 14:48:24 +02:00
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
c75b30d58f
gnu: Add r-catch.
...
* gnu/packages/bioinformatics.scm (r-catch): New variable.
2021-09-01 14:53:36 +02:00
4abf226833
gnu: Add scregseg.
...
* gnu/packages/bioinformatics.scm (scregseg): New variable.
2021-08-31 23:11:06 +02:00
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
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
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
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
7712154ccb
gnu: Add python-coolbox.
...
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
2021-08-30 18:29:57 +02:00
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
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
e85b35070c
gnu: Add python-pybbi.
...
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
2021-08-30 18:29:56 +02:00
db13eb962f
gnu: Add python-strawc.
...
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
2021-08-27 13:37:29 +02:00
17c765e2e1
gnu: Add r-cytonorm.
...
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
2021-08-27 13:37:29 +02:00
f66759e0b2
gnu: Add ivar.
...
* gnu/packages/bioinformatics.scm (ivar): New variable.
2021-08-25 11:22:02 +02:00
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
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
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
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
2ab5d08fbe
gnu: Add r-spectre.
...
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
2021-08-03 10:43:08 +02:00
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
99ca1ae4f8
gnu: Add segemehl.
...
* gnu/packages/bioinformatics.scm (segemehl): New variable.
2021-07-26 11:08:13 +02:00
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
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
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
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
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
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
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
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
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
cc4906d13b
gnu: Add htslib-1.10.
...
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22 10:50:58 +03:00
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
73830b5da3
gnu: Add r-battenberg.
...
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21 13:36:08 +02:00
ed636babfa
gnu: Add r-ascat.
...
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
2021-07-21 13:36:08 +02:00
690df95d1a
gnu: Add nanosv.
...
* gnu/packages/bioinformatics.scm (nanosv): New variable.
2021-07-21 13:36:08 +02:00
2b665b8a49
gnu: Add python-pyvcf.
...
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
2021-07-21 13:36:08 +02:00
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
18a02fe7ca
gnu: Add tombo.
...
* gnu/packages/bioinformatics.scm (tombo): New variable.
2021-07-21 13:36:07 +02:00
0e47fcced4
Merge branch 'master' into core-updates
2021-07-18 19:50:01 +02:00
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
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
b17ee44212
gnu: Do not import (gnu packages commencement).
...
Line introduced in 4efbf56e53
2021-07-01 17:13:13 +02:00
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
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
44bccf414b
gnu: Add perl-cworld-dekker.
...
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
2021-06-22 08:40:56 +02:00
8a62d8685a
gnu: Add python-iced.
...
* gnu/packages/bioinformatics.scm (python-iced): New variable.
2021-06-21 13:02:39 +02:00
6f9a80b331
Merge branch 'master' into core-updates
...
Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a27712964df69a4604d43c0e
2021-06-19 17:38:47 +02:00
748d3a2b8a
gnu: Add python-cgatcore.
...
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
2021-06-14 23:13:56 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
0928e55266
gnu: Add fit-sne.
...
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
2021-06-03 12:22:29 +02:00
011d586c2c
gnu: Add biobambam2.
...
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
2021-06-02 13:54:15 +02:00
18e0081045
gnu: Add libmaus2.
...
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
2021-06-02 13:54:15 +02:00
7ae2b1f2dc
gnu: Add bamutils.
...
* gnu/packages/bioinformatics.scm (bamutils): New variable.
2021-06-01 13:14:38 +02:00
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
d1e1c02e28
gnu: piranha: Use git-version.
...
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
2021-05-31 16:10:00 +02:00
8c033085cc
gnu: r-chipkernels: Use git-version and git-file-name.
...
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:09:35 +02:00
3acfbd4811
gnu: f-seq: Use git-version and git-file-name.
...
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:09:07 +02:00
09b50a6ec2
gnu: bismark: Use git-file-name.
...
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
2021-05-31 16:08:47 +02:00
f383f9e311
gnu: filevercmp: Use git-version.
...
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
2021-05-31 16:08:12 +02:00
a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
2021-05-31 15:53:20 +02:00
b0ecd6cea9
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.
...
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 15:46:30 +02:00
c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
2021-05-31 15:39:49 +02:00
7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
2021-05-31 15:39:49 +02:00
36cb01066c
gnu: r-copyhelper: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31 15:39:47 +02:00
31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
2021-05-31 15:39:00 +02:00
0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
2021-05-31 15:39:00 +02:00
cc1dbea883
gnu: r-annotationfilter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
2021-05-31 15:39:00 +02:00
67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
2021-05-31 15:39:00 +02:00
b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
2021-05-31 15:39:00 +02:00
bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
2021-05-31 15:39:00 +02:00
7360dea624
gnu: r-rcas: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
2021-05-31 15:39:00 +02:00
45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
2021-05-31 15:38:59 +02:00
Ricardo Wurmus
Tobias Geerinckx-Rice
Josselin Poiret
Mathieu Othacehe
Arun Isaac
Efraim Flashner
zimoun
Hong Li
Mădălin Ionel Patrașcu
Maxim Cournoyer
Ludovic Courtès
Nicolas Goaziou
Marius Bakke
Sarah Morgensen
Vagrant Cascadian
Julien Lepiller
Felix Gruber
Lars-Dominik Braun
Charles
Roel Janssen
Maxime Devos