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3457 Commits

Author SHA1 Message Date
Arun Isaac
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
Arun Isaac
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
Arun Isaac
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
Arun Isaac
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
Arun Isaac
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
Arun Isaac
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
Arun Isaac
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
Arun Isaac
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
33fe027f91
gnu: Add r-giotto. 
* gnu/packages/bioinformatics.scm (r-giotto): New variable.
 2022-04-26 09:48:14 +02:00
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
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
zimoun
6413d0898b
gnu: Add r-copykat. 
* gnu/packages/bioinformatics.scm (r-copykat): New variable.
 2022-04-11 16:11:45 +02:00
Efraim Flashner
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
Hong Li
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Efraim Flashner
345f79b2cf
gnu: freebayes: Fix test suite. 
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
 2022-04-04 22:58:25 +03:00
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
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
Efraim Flashner
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
Arun Isaac
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
Arun Isaac
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
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
ca588fdfde
gnu: Add r-scopeloomr. 
* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
 2022-03-09 11:35:59 +01:00
Ludovic Courtès
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
Efraim Flashner
a6867b2d98
gnu: minimap2: Update to 2.24. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
 2022-02-27 11:42:30 +02:00
Ricardo Wurmus
3fb78caa55
gnu: Add r-dyngen. 
* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
 2022-02-22 18:48:30 +01:00
Marius Bakke
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
Ricardo Wurmus
7fc8a6faf6
gnu: Add scvelo. 
* gnu/packages/bioinformatics.scm (scvelo): New variable.
 2022-01-31 16:07:40 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Marius Bakke
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
Marius Bakke
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
zimoun
ce291b193c
gnu: Add r-scseqcomm. 
* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
 2022-01-21 15:53:18 +01:00
zimoun
dac6b53c7e
gnu: Add r-icellnet. 
* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
 2022-01-21 15:53:18 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
61d7da5a1f
gnu: Add r-doubletfinder. 
* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
 2022-01-20 12:00:03 +01:00
Marius Bakke
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
Maxim Cournoyer
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
Ricardo Wurmus
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
Sarah Morgensen
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
Sarah Morgensen
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
Maxim Cournoyer
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
Maxim Cournoyer
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
Maxim Cournoyer
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
Maxim Cournoyer
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Vagrant Cascadian
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
Vagrant Cascadian
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
Vagrant Cascadian
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
Vagrant Cascadian
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
Vagrant Cascadian
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
Ricardo Wurmus
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
Marius Bakke
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
Ludovic Courtès
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
Ricardo Wurmus
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
Mathieu Othacehe
32750e8c3e
Merge remote-tracking branch 'signed/master' into core-updates 2021-12-10 21:49:25 +01:00
Arun Isaac
af5fa4d202
gnu: Add ccwl. 
* gnu/packages/bioinformatics.scm (ccwl): New variable.
 2021-12-10 15:26:59 +05:30
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
f0cc0e8f30
gnu: imp: Build with default cmake. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
 2021-12-09 14:39:22 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
0b8a75cc3a
gnu: Add samtools-1.2. 
* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
b835d10d61
gnu: paml: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
738f22fa06
gnu: imp: Disable tests. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test
suite.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
4195a877cb
gnu: Add pbcopper. 
* gnu/packages/bioinformatics.scm (pbcopper): New variable.
 2021-12-07 16:00:22 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
16474f85cf
gnu: taxtastic: Update to 0.9.2. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases;  adjust
'prepare-directory phase.
 2021-12-07 15:13:06 +01:00
Ricardo Wurmus
00ba04020e
gnu: taxtastic: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
 2021-12-07 15:12:15 +01:00
Ricardo Wurmus
58fecfd18e
gnu: python-dendropy: Update to 4.5.1. 
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1.
[arguments]: Skip failing tests.
 2021-12-07 14:53:37 +01:00
Ricardo Wurmus
2da567d137
gnu: python-cooler: Use python-cytoolz-for-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz with python-cytoolz-for-cooler.
 2021-12-07 13:24:58 +01:00
Ricardo Wurmus
899121f4d6
gnu: phylip: Update to 3.697. 
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
 2021-12-07 13:05:53 +01:00
Ricardo Wurmus
e86fe9801e
gnu: phylip: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
 2021-12-07 13:05:35 +01:00
Ricardo Wurmus
125fdc3ba4
gnu: phylip: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
 2021-12-07 13:05:15 +01:00
Ricardo Wurmus
4561ca7f4e
gnu: subread: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
 2021-12-07 12:59:51 +01:00
Ricardo Wurmus
96b2be833d
gnu: subread: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
 2021-12-07 12:59:36 +01:00
Ricardo Wurmus
9a03587b62
gnu: subread: Update home page.. 
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
 2021-12-07 12:55:08 +01:00
Ricardo Wurmus
aa25c9b1a4
gnu: subread: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
 2021-12-07 12:54:48 +01:00
Ricardo Wurmus
06fca01968
gnu: hisat: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
 2021-12-07 11:51:10 +01:00
Ricardo Wurmus
2f7287b3a7
gnu: hisat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
9dc727f827
gnu: hisat: Remove invalid characters. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
478e3e714a
gnu: crossmap: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b5c9afb7c5
gnu: Remove python2-bx-python. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
699b443c86
gnu: python-bx-python: Update to 0.8.12. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12.
[propagated-inputs]: Remove python-six.
[arguments]: Remove.  Tests are still not run, though.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
4b4ab4ce4d
gnu: Remove pbtranscript-tofu. 
Upstream has disappeared and it depends on Python 2, which is no longer
supported.

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

* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for
missing trailing slash.
* gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
 2021-12-05 14:02:10 +01:00
Marius Bakke
b507cc49ab
gnu: python-pyvcf: Fix bytecode compilation. 
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to
patch sample script.
 2021-12-05 14:02:10 +01:00
Efraim Flashner
e70e26423b
gnu: minimap2: Update to 2.23. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
 2021-12-05 11:51:10 +02:00
Ricardo Wurmus
1e7bd5e679
gnu: salmon: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove
reference to %build-inputs.
 2021-12-05 00:49:06 +01:00
Ricardo Wurmus
98d2abe523
gnu: sailfish: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove
references to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
39e2a84f52
gnu: sailfish: Simplify snippet. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
b0fd09f856
gnu: piranha: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove
references to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
01d2e2b334
gnu: piranha: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T
from build phases.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
502538c6e4
gnu: emboss: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove
reference to %build-inputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
2657bdc100
gnu: vcftools: Replace references to %outputs. 
* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove
references to %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
eec1bdcd9e
gnu: seqan-1: Use gexp for builder. 
* gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
2c1c75a56c
gnu: seqan-2: Use gexp for builder. 
* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
 2021-12-04 19:54:28 +01:00
Ricardo Wurmus
f41576c09f
gnu: sra-tools: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead
of referencing %build-inputs.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
f33e490334
gnu: preseq: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to
%outputs and %build-inputs by using a gexp.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
8a446f5e41
gnu: preseq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
 2021-12-04 19:54:27 +01:00
Ricardo Wurmus
cc491eab7e
gnu: plink-ng: Enable tests. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
 2021-12-04 16:00:08 +01:00
Ricardo Wurmus
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:35:28 +01:00
Ricardo Wurmus
88bb81b515
gnu: plink: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
 2021-12-04 15:31:31 +01:00
Ricardo Wurmus
e920101141
gnu: plink: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 15:31:08 +01:00
Ricardo Wurmus
a4e7475edc
gnu: rsem: Update to 1.3.3. 
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
 2021-12-04 15:27:39 +01:00
Ricardo Wurmus
c45c909026
gnu: rsem: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
 2021-12-04 15:26:48 +01:00
Ricardo Wurmus
5e0bcba57b
gnu: rsem: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
 2021-12-04 15:26:01 +01:00
Ricardo Wurmus
23975fe27a
gnu: rsem: Remove trailing #T from snippet. 
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
 2021-12-04 15:25:26 +01:00
Ricardo Wurmus
cfaf37d10b
gnu: prodigal: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-04 15:13:11 +01:00
Ricardo Wurmus
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
 2021-12-04 15:11:28 +01:00
Ricardo Wurmus
e128839a94
gnu: prank: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
 2021-12-04 15:11:04 +01:00
Ricardo Wurmus
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
 2021-12-04 12:42:51 +01:00
Ricardo Wurmus
114eb987cb
gnu: mash: Replace references to %build-inputs. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
 2021-12-04 00:32:01 +01:00
Ricardo Wurmus
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs. 
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
 2021-12-04 00:31:20 +01:00
Ricardo Wurmus
a6b6084649
gnu: mash: Simplify snippet. 
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
 2021-12-04 00:30:44 +01:00
Ricardo Wurmus
31409a4af7
gnu: mafft: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
 2021-12-04 00:22:27 +01:00
Ricardo Wurmus
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
 2021-12-04 00:21:27 +01:00
Ricardo Wurmus
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
 2021-12-04 00:19:08 +01:00
Ricardo Wurmus
7c2ee27360
gnu: fastp: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
 2021-12-04 00:16:10 +01:00
Ricardo Wurmus
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
 2021-12-04 00:06:43 +01:00
Ricardo Wurmus
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
 2021-12-04 00:03:54 +01:00
Ricardo Wurmus
62e0641892
gnu: fxtract: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
 2021-12-04 00:02:20 +01:00
Ricardo Wurmus
4f03151ca4
gnu: delly: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-04 00:00:26 +01:00
Ricardo Wurmus
3601fcbf65
gnu: libbigwig: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-03 23:57:24 +01:00
Ricardo Wurmus
fd607a9efa
gnu: cd-hit: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
 2021-12-03 23:56:11 +01:00
Ricardo Wurmus
c40852a227
gnu: bowtie1: Replace reference to %outputs. 
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-03 23:54:10 +01:00
Ricardo Wurmus
a47a90b900
gnu: bowtie: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
 2021-12-03 23:52:43 +01:00
Ricardo Wurmus
f5c38ee45f
gnu: bless: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp.  Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
 2021-12-03 23:51:16 +01:00
Ricardo Wurmus
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases. 
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
 2021-12-03 23:48:46 +01:00
Ricardo Wurmus
0e09065460
gnu: bedtools: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
 2021-12-03 23:36:18 +01:00
Ricardo Wurmus
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs. 
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
 2021-12-03 23:26:48 +01:00
Ricardo Wurmus
ce9bfcddb5
gnu: imp: Update to 2.15.0. 
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
 2021-12-03 22:29:52 +01:00
Ricardo Wurmus
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
 2021-12-03 14:55:38 +01:00
Ricardo Wurmus
d0aa14a43d
gnu: Add vbz-compression. 
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
 2021-12-03 14:55:38 +01:00
Ricardo Wurmus
6d4f260166
gnu: bamutils: Update to 1.0.14. 
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
 2021-12-03 13:56:02 +01:00
Ricardo Wurmus
673cc29908
gnu: bamutils: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
361e0d9f27
gnu: bamm: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
7fb5bfc54f
gnu: python-plastid: Update to 0.5.1. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
b7aaf6c418
gnu: ivar: Disable parallel tests. 
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
 2021-12-03 13:48:41 +01:00
Ricardo Wurmus
aa2d5ca02e
gnu: Remove python2-biom-format. 
There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
 2021-12-03 13:31:32 +01:00
Ricardo Wurmus
a2423c0ca4
gnu: ribodiff: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
 2021-12-02 18:32:33 +01:00
Ricardo Wurmus
1123d25830
gnu: ribodiff: Disable broken test. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
 2021-12-02 18:32:10 +01:00
Ricardo Wurmus
31d372cd8a
gnu: khmer: Fix build with Python 3.8. 
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
 2021-12-02 18:24:31 +01:00
Ricardo Wurmus
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
 2021-12-02 18:02:07 +01:00
Ricardo Wurmus
28ad55a59d
gnu: pardre: Update to 2.2.5. 
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI. 
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
a8fff63daa
gnu: Add python-mygene. 
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
 2021-12-02 11:57:28 +01:00
Ricardo Wurmus
b15a525703
gnu: Add python-biothings-client. 
* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
 2021-12-02 11:57:13 +01:00
Ricardo Wurmus
37c475ebc0
gnu: prinseq: Fix use of SEARCH-INPUT-FILE. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
 2021-12-02 11:26:55 +01:00
Ricardo Wurmus
d53679c531
gnu: Remove couger. 
This package has been moved to the Guix Past channel.

* gnu/packages/bioinformatics.scm (couger): Remove variable.
 2021-12-02 00:32:12 +01:00
Ricardo Wurmus
173a2998d9
gnu: r-umi4cpackage: Embed references to perl and bowtie2. 
* gnu/packages/bioinformatics.scm (r-umi4cpackage)[arguments]: Add build
phases to patch calls of bowtie2 and perl.
[inputs]: Add perl and bowtie.
[synopsis]: Remove trailing period.
 2021-11-30 16:46:17 +01:00
Ludovic Courtès
b15e543d30
Merge branch 'master' into core-updates-frozen 2021-11-23 11:29:38 +01:00
Ricardo Wurmus
e74bcbc64f
gnu: python-scanpy: Set PYTHONPATH variable. 
This is a follow-up to commit 664721422c.

* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Set PYTHONPATH
variable during the build as GUIX_PYTHONPATH does not have the intended
effect.
 2021-11-21 09:07:50 +01:00
Ricardo Wurmus
6c9bbf8071
gnu: python-scanpy: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2.
[arguments]: Disable test_clustermap test.
 2021-11-21 09:07:50 +01:00
Ricardo Wurmus
1a9665743b
gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
GUIX_PYTHONPATH.
 2021-11-21 00:40:34 +01:00
Ricardo Wurmus
664721422c
gnu: python-scanpy: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use
GUIX_PYTHONPATH instead of PYTHONPATH.
 2021-11-21 00:39:57 +01:00
Ricardo Wurmus
55870e86d9
gnu: multiqc: Remove sanity check. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
 2021-11-21 00:39:09 +01:00
Ricardo Wurmus
e2ca652c98
gnu: multiqc: Use GUIX_PYTHONPATH. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH
with GUIX_PYTHONPATH.
 2021-11-21 00:39:05 +01:00
Ricardo Wurmus
c618f4a9cc
gnu: pigx-bsseq: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
 2021-11-20 16:31:32 +01:00
Vagrant Cascadian
a8eea7a51e
gnu: qtltools: Fix typo. 
* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
  to go" to "allows going".
 2021-11-18 14:20:07 -08:00
Ricardo Wurmus
dddc90a363
gnu: shorah: Use GUIX_PYTHONPATH in wrapper. 
* gnu/packages/bioinformatics.scm (shorah)[arguments]: Wrap executable with
GUIX_PYTHONPATH.
 2021-11-18 19:25:16 +00:00
Ludovic Courtès
3a317f7476
Merge branch 'master' into core-updates-frozen 2021-11-17 23:43:14 +01:00
Julien Lepiller
0a9a00b34c
gnu: pplacer: Fix build. 
* gnu/packages/bioinformatics.scm (pplacer): Add missing input.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-11-16 15:43:51 +02:00
Ricardo Wurmus
616bcc9c0b
gnu: python-scanpy: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
 2021-11-15 15:21:06 +00:00
Ricardo Wurmus
a0fc9e38fa
gnu: ciri-long: Move Cython to native inputs. 
* gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from
here...
[native-inputs]: ...to here.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
c4e5fabb6e
gnu: ciri-long: Fix reference to ccs. 
* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
6be47c5bc5
gnu: Add circtools. 
* gnu/packages/bioinformatics.scm (circtools): New variable.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
b8c9f061e1
gnu: Add bioparser. 
* gnu/packages/bioinformatics.scm (bioparser): New variable.
 2021-11-11 15:39:19 +00:00
Ricardo Wurmus
4052310e91
gnu: Add biosoup. 
* gnu/packages/bioinformatics.scm (biosoup): New variable.
 2021-11-11 15:39:19 +00:00
Efraim Flashner
1c94392a13
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-11-08 09:06:14 +02:00
Ricardo Wurmus
d54a4285ea
gnu: bedtools-2.18: Fix build with newer toolchain. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase
'compatibility, fixing syntax quirks that are problematic with newer
toolchains.
[native-inputs]: Do not inherit.
[inherit]: Do not inherit.
 2021-11-03 21:07:29 +00:00
Efraim Flashner
bc5155b952
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-10-31 14:49:47 +02:00
Ricardo Wurmus
41e5c12c4a
gnu: sailfish: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 21:38:25 +00:00
Ricardo Wurmus
1bf55a4850
gnu: sailfish: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in
build phases...
[inputs]: ...and in the origin snippet of "rapmap".
 2021-10-24 21:37:39 +00:00
Ricardo Wurmus
4392783232
gnu: sailfish: Do not attempt to unpack a directory. 
patch-and-repack no longer outputs a compressed archive when the input was a
directory.

* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Adjust build phase
'prepare-rapmap.
 2021-10-24 21:35:57 +00:00
Ricardo Wurmus
57c233b37b
gnu: jellyfish: Remove Ruby bindings. 
These bindings no longer build and we have no package that would need them.

* gnu/packages/bioinformatics.scm (jellyfish)[outputs]: Remove "ruby" output.
[arguments]: Remove option for building Ruby bindings.
[native-inputs]: Remove ruby.
 2021-10-24 21:34:26 +00:00
Ricardo Wurmus
da526f33f2
gnu: cutadapt: Regenerate Cython files. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
 2021-10-24 21:23:20 +00:00
Ricardo Wurmus
4faca03bed
gnu: python-dnaio: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
 2021-10-24 19:47:20 +00:00
Ricardo Wurmus
238f47c76f
gnu: macs: Fix build by setting HOME. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
 2021-10-24 19:09:35 +00:00
Ricardo Wurmus
1d01043a4f
gnu: methyldackel: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
 2021-10-24 19:01:22 +00:00
Ricardo Wurmus
2820b03509
gnu: methyldackel: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
 2021-10-24 19:00:53 +00:00
Ricardo Wurmus
cc331ad7eb
gnu: flexbar: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:50:09 +00:00
Ricardo Wurmus
084bdf9d69
gnu: flexbar: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
 2021-10-24 18:49:43 +00:00
Ricardo Wurmus
d0a1d798ee
gnu: bwa: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
 2021-10-24 18:48:53 +00:00
Ricardo Wurmus
2da99b671e
gnu: bwa: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
 2021-10-24 18:48:20 +00:00
Ricardo Wurmus
724972bcca
gnu: bowtie1: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:47:45 +00:00
Ricardo Wurmus
f336cc4fe7
gnu: bowtie: Replace invalid characters. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
 2021-10-24 18:44:57 +00:00
Ricardo Wurmus
e5a26a1f02
gnu: bowtie: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
 2021-10-24 16:59:39 +00:00
Ricardo Wurmus
2ec601580b
gnu: bowtie: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
 2021-10-24 16:58:58 +00:00
Ricardo Wurmus
973b21aa6a
gnu: Add r-umi4cpackage. 
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
 2021-10-24 13:45:46 +00:00
Ricardo Wurmus
42873c2b06
gnu: tbb-for-salmon: Rename. 
* gnu/packages/tbb.scm (tbb-for-salmon): Rename this variable...
(tbb-2020): ...to this.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Rename it.
 2021-10-24 13:28:05 +00:00
Ricardo Wurmus
4a0cd6297a
gnu: Add qtltools. 
* gnu/packages/bioinformatics.scm (qtltools): New variable.
 2021-10-22 21:29:25 +00:00
Ricardo Wurmus
a8bac123f0
gnu: Add gdc-client. 
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
 2021-10-21 14:49:01 +00:00
Ricardo Wurmus
f65917f607
gnu: Add r-shaman. 
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
 2021-10-21 14:34:35 +00:00
Ricardo Wurmus
4885f40b80
gnu: Add r-misha. 
* gnu/packages/bioinformatics.scm (r-misha): New variable.
 2021-10-21 14:25:44 +00:00
Ricardo Wurmus
42c9b75b25
gnu: Add ciri-long. 
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
 2021-10-21 13:39:36 +00:00
Ricardo Wurmus
10664fcc8c
gnu: python-biopython: Update to 1.76. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.76.
(python-biopython-1.73): New variable.
(instrain)[inputs]: Replace python-biopython with python-biopython-1.73.
 2021-10-21 13:33:51 +00:00
Ricardo Wurmus
36cf0253a9
gnu: instrain: Update to 1.5.4. 
* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
 2021-10-21 13:32:37 +00:00
Ricardo Wurmus
57841a91f5
gnu: Add python-bwapy. 
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
 2021-10-21 12:23:25 +00:00
Ricardo Wurmus
6526c35df5
gnu: Add python-pyspoa. 
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
 2021-10-21 12:23:22 +00:00
Ricardo Wurmus
174c29a8e0
gnu: salmon: Use older version of TBB. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Define
HAVE_NUMERIC_LIMITS128; compute TBB_VERSION.
[inputs]: Replace tbb with tbb-for-salmon.
 2021-10-19 06:28:30 +00:00
Mathieu Othacehe
a1eca979fb
Merge remote-tracking branch 'origin/master' into core-updates-frozen. 2021-10-12 17:46:23 +00:00
Felix Gruber
9101c7bf8e
gnu: clipper: Disable non-deterministic test. 
This test fails/succeeds non-deterministically.

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

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

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

525 packages have been updated.

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

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

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

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

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

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

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

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

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

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-09-06 10:47:54 +02:00
Ricardo Wurmus
c75b30d58f
gnu: Add r-catch. 
* gnu/packages/bioinformatics.scm (r-catch): New variable.
 2021-09-01 14:53:36 +02:00
Ricardo Wurmus
4abf226833
gnu: Add scregseg. 
* gnu/packages/bioinformatics.scm (scregseg): New variable.
 2021-08-31 23:11:06 +02:00
Ricardo Wurmus
a1ee212184
gnu: python-strawc: Propagate pybind11. 
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Ricardo Wurmus
55cb5a62a1
gnu: python-scanpy: Propagate sinfo. 
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Marius Bakke
c4133c43c7
Merge branch 'master' into core-updates-frozen 
Conflicts:
	gnu/packages/algebra.scm
	gnu/packages/games.scm
	gnu/packages/golang.scm
	gnu/packages/kerberos.scm
	gnu/packages/mail.scm
	gnu/packages/python.scm
	gnu/packages/ruby.scm
	gnu/packages/scheme.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
 2021-08-12 00:30:27 +02:00
Marius Bakke
b029be2ee0
Merge branch 'master' into core-updates-frozen 
Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/cmake.scm
	gnu/packages/curl.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/gpodder.scm
	gnu/packages/music.scm
	gnu/packages/patches/glibc-bootstrap-system.patch
	gnu/packages/python-xyz.scm
	gnu/packages/shells.scm
	gnu/packages/statistics.scm
 2021-07-29 22:34:57 +02:00
Ricardo Wurmus
7712154ccb
gnu: Add python-coolbox. 
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus
b105655670
gnu: python-scanpy: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
 2021-08-30 18:29:57 +02:00