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3166 Commits

Author SHA1 Message Date
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