d3e982dccb
gnu: Fix typos.
...
* gnu/packages/emacs-xyz.scm (emacs-piem)[description]: Fix use of "This
packages".
* gnu/packages/tex.scm (texlive-hardwrap)[description]: Fix spelling of
"arbitrary".
* gnu/packages/cran.scm (r-shinymanager)[description]: Fix spelling of
"authentication".
* gnu/packages/lisp-xyz.scm (sbcl-utils-kt)[description]: Fix spelling of
"developed".
* gnu/packages/crates-io.scm (rust-fs-utils-1)[description]: Fix spelling of
"filesystem".
[synopsis]: Likewise.
* gnu/packages/haxe.scm (neko)[description]: Fix spelling of "functions".
* gnu/packages/animation.scm (swftools)[description]: Fix needless
pluralization of "information".
* gnu/packages/lisp-xyz.scm (sbcl-slot-extra-options)[description]: Fix
spelling of "inheritance".
* gnu/packages/emacs-xyz.scm (emacs-js-comint)[description]: Fix spelling of
"interpreter".
* gnu/packages/coq.scm (coq-mathcomp-finmap)[description]: Fix spelling of
"library".
* gnu/services/lightdm.scm (lightdm-configuration): Fix spelling of
"mechanism".
* gnu/packages/emacs-xyz.scm (emacs-citar-org-roam)[synopsis]: Fix spelling of
"package".
* gnu/packages/games.scm (freerct)[description]: Fix spelling of
"responsibilities".
* gnu/packages/statistics.scm (r-mixedpower)[description]: Fix spelling of
"separate".
* gnu/packages/accessibility.scm (espeakup)[description]: Fix spelling of
"speech".
* gnu/packages/bioinformatics.scm (r-skitools)[synopsis]: Fix spelling of
"utilities".
* gnu/packages/golang.scm (go-github-com-savsgio-gotils)[synopsis]: Fix
spelling of "utilities".
[description]: Likewise.
* gnu/system.scm (boot-file-system-service os): Fix spelling of "utilities".
2022-10-23 17:03:09 -07:00
f24b66bf4a
gnu: pigx-sars-cov-2: Update to 0.0.8.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.8.
[arguments]: Add build phase 'unpack-databases; enable tests.
[native-inputs]: Add origins for databases; remove automake and autoconf.
[inputs]: Add r-data-table, r-deconvr, r-htmltools, r-jsonlite, r-knitr, and
r-mass.
2022-10-08 12:06:41 +02:00
020dc0a1f1
gnu: plink: Change origin URL.
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pngu.mgh.harvard.edu seems to time out.
* gnu/packages/bioinformatics.scm (plink)[origin]. Change URL.
2022-10-06 15:08:02 +01:00
fd6cd9de86
gnu: Add megahit.
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* gnu/packages/bioinformatics.scm (megahit): New variable.
2022-10-05 17:59:04 +02:00
be1d561f1a
gnu: Add cd-hit-auxtools.
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* gnu/packages/bioinformatics.scm (cd-hit-auxtools): New variable.
2022-10-05 14:28:24 +02:00
3f627bf56b
gnu: cd-hit: Update to 4.8.1.
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* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.8.1.
[arguments]: Do not use quasiquote; remove trailing #T from build phases.
[inputs]: Add zlib.
2022-10-05 13:47:57 +02:00
9ed65e6af7
gnu: kaiju: Update to 1.9.0.
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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0.
[arguments]: Use gexps; wrap scripts in install phase.
[inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip,
python-wrapper, tar, and wget.
2022-10-04 23:10:56 +02:00
1266b9ed11
gnu: salmon: Update to 1.9.0.
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* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0.
[arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish
itlib headers.
[inputs]: Use new label-less list; move pufferfish origin from here...
[native-inputs]: ...to here.
2022-09-30 22:43:21 +02:00
729ce5fcf8
gnu: Add centrifuge.
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* gnu/packages/bioinformatics.scm (centrifuge): New variable.
2022-09-30 16:59:18 +02:00
1ee2d117d8
gnu: blast+: Build reproducibly.
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Fixes <https://issues.guix.gnu.org/42141 >.
* gnu/packages/bioinformatics.scm (blast+)[source]: Do not record kernel
version and use fix set of random numbers.
2022-09-29 23:21:16 +02:00
c1716ab6ec
gnu: Add r-compgenomrdata.
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* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
2022-09-26 17:21:57 +02:00
cbe8391d7c
gnu: Add mudskipper.
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* gnu/packages/bioinformatics.scm (mudskipper): New variable.
2022-09-23 00:21:40 +02:00
1a1ff7ed8f
gnu: python-cooler: Skip broken test.
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* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add another
patch for tests/test_util.py.
2022-09-21 22:19:33 +02:00
cd5bbb9b42
gnu: python-cooler: Do not use flake8.
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* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add build phase
'do-not-use-flake8.
2022-09-21 22:19:33 +02:00
d871080a41
gnu: Add r-chromunity.
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* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
2022-09-21 11:09:46 +02:00
a7f6392caa
gnu: Add r-skitools.
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* gnu/packages/bioinformatics.scm (r-skitools): New variable.
2022-09-21 11:09:46 +02:00
af663c9e48
gnu: Add r-gchain.
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* gnu/packages/bioinformatics.scm (r-gchain): New variable.
2022-09-21 11:09:46 +02:00
6ad4d74aca
gnu: Add r-gtrack.
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* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
2022-09-21 11:09:46 +02:00
29634a4ce3
gnu: Add r-bamutils.
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* gnu/packages/bioinformatics.scm (r-bamutils): New variable.
2022-09-21 11:09:45 +02:00
4bd64dde2b
gnu: Add r-gutils.
...
* gnu/packages/bioinformatics.scm (r-gutils): New variable.
2022-09-21 11:09:41 +02:00
8084e3bdb3
gnu: python-pyvcf: Update to 0.6.8-0.476169c.
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* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
2022-09-20 17:02:34 +02:00
9ed635cd9a
gnu: python-pyvcf: Use older setuptools.
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* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Replace
python-setuptools with python-setuptools-for-tensorflow.
2022-09-20 17:02:34 +02:00
b736af1824
gnu: catch-framework2: Rename variable to catch2.
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Automated with:
git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i
2022-09-15 20:15:56 -04:00
a7af25ad31
gnu: kraken2: Update to 2.1.2.
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* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2.
2022-09-13 17:35:38 +02:00
ad1d3f98b1
gnu: Add comments to the bottom of a few package modules.
...
This will hopefully discourage patches which add new packages to the bottom of
files, as this increases the likelihood of conflicts when applying patches.
If there are more specific ways that packages should be arranged in specific
modules, this message can be updated accordingly.
* gnu/packages/bioconductor.scm: Add comment discouraging adding packages to
the bottom of the file.
* gnu/packages/bioinformatics.scm: ditto.
* gnu/packages/cran.scm: ditto.
* gnu/packages/crates-io.scm: ditto.
* gnu/packages/emacs-xyz.scm: ditto.
* gnu/packages/golang.scm: ditto.
* gnu/packages/guile-xyz.scm: ditto.
* gnu/packages/haskell-xyz.scm: ditto.
* gnu/packages/java.scm: ditto.
* gnu/packages/julia-xyz.scm: ditto.
* gnu/packages/lisp-xyz.scm: ditto.
* gnu/packages/ocaml.scm: ditto.
* gnu/packages/perl.scm: ditto.
* gnu/packages/python-science.scm: ditto.
* gnu/packages/python-xyz.scm: ditto.
* gnu/packages/ruby.scm: ditto.
* gnu/packages/tex.scm: ditto.
2022-09-10 10:45:27 +01:00
453e7dd8c4
gnu: tombo: Disable tests.
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* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
2022-09-07 17:36:42 +02:00
36445e4d96
gnu: pigx-bsseq: Update to 0.1.8.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.8.
2022-08-31 09:12:03 +02:00
8c5246677c
gnu: r-dyngen: Update to 1.0.4.
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* gnu/packages/bioinformatics.scm (r-dyngnen): Update to 1.0.4.
[source]: Change to cran-uri source.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net >
2022-08-30 23:01:58 +02:00
d26b29d263
gnu: Add flair.
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* gnu/packages/bioinformatics.scm (flair): New variable.
2022-08-23 13:30:52 +02:00
8d42898572
gnu: python-mappy: Update to 2.24.
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* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
2022-08-23 13:29:17 +02:00
f3a7d43281
gnu: Add r-kbet.
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* gnu/packages/bioinformatics.scm (r-kbet): New variable.
2022-08-18 12:21:07 +02:00
8aab1f7c73
gnu: Add go-github-com-biogo-biogo.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable.
2022-08-16 16:52:15 +02:00
2407416d0f
gnu: Add go-github-com-biogo-hts-fai.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable.
2022-08-16 16:50:16 +02:00
31e0ac6dcf
gnu: Add go-github-com-biogo-hts-csi.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable.
2022-08-16 16:50:01 +02:00
b4f389e1b9
gnu: Add go-github-com-biogo-hts-cram.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable.
2022-08-16 16:44:58 +02:00
e9bec5bd40
gnu: Add go-github-com-biogo-hts-bgzf.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable.
2022-08-16 16:28:33 +02:00
bb162a5103
gnu: Add go-github-com-biogo-hts-tabix.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable.
2022-08-16 16:28:23 +02:00
4645a5d3f6
gnu: Add go-github-com-biogo-hts-sam.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
2022-08-16 16:28:11 +02:00
b986325b13
gnu: Add go-github-com-biogo-hts-bam.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
2022-08-16 16:23:04 +02:00
2345cd49de
gnu: Add go-github-com-biogo-store-step.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
2022-08-16 16:18:57 +02:00
c42745ba39
gnu: Add go-github-com-biogo-store-llrb.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
2022-08-16 16:18:48 +02:00
5fae9e158d
gnu: Add go-github-com-biogo-store-kdtree.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
2022-08-16 16:18:40 +02:00
a33ee9bd51
gnu: Add go-github-com-biogo-store-interval.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
2022-08-16 16:18:31 +02:00
2b4dcc477b
gnu: Add go-github-com-biogo-graph.
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* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
2022-08-16 16:09:54 +02:00
872e17ddc1
gnu: Add stpipeline.
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* gnu/packages/bioinformatics.scm (stpipeline): New variable.
2022-08-16 15:22:07 +02:00
9c2400c282
gnu: Add python-taggd.
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* gnu/packages/bioinformatics.scm (python-taggd): New variable.
2022-08-16 15:22:07 +02:00
752be79bf3
gnu: htseq: Update to 2.0.2.
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* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.2.
[source]: Fetch from git repository.
[arguments]: Delete 'build phase; run tests with pytest in 'check phase.
[propagated-inputs]: Add python-matplotlib and python-pysam.
[inputs]: Remove python-matplotlib and python-pysam.
[native-inputs]: Add python-pandas, python-pytest, python-scipy, and swig.
[synopsis]: Update.
[description]: Update.
2022-08-16 15:22:06 +02:00
c3c2dfdb5e
gnu: plink-ng: Build sources from 2.0 directory
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* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Disable tests; adjust
make flags; enter 2.0 directory in 'chdir phase; replace 'install phase.
[inputs]: Add zstd:lib.
2022-08-15 18:08:20 +02:00
26bdefd172
gnu: Add r-liana.
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* gnu/packages/bioinformatics.scm (r-liana): New variable.
2022-08-10 15:44:28 +02:00
fd4b8e9873
gnu: Add r-omnipathr/devel.
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* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
2022-08-10 15:44:28 +02:00
Vagrant Cascadian