1369b53d49
gnu: seqmagick: Update to 0.8.4.
...
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
2022-12-13 00:08:54 +01:00
461dff2651
gnu: python-cgatcore: Update to 0.6.14.
...
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
2022-12-13 00:08:54 +01:00
b72df3bbb3
gnu: python-dna-features-viewer: Update to 3.1.1.
...
* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
2022-12-13 00:07:23 +01:00
b66b6bdf70
gnu: python-hicexplorer: Update to 3.7.2.
...
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
2022-12-13 00:07:23 +01:00
c3e330cf36
gnu: python-pygenometracks: Update to 3.5.
...
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
2022-12-13 00:07:22 +01:00
6e9518e201
gnu: python-hicmatrix: Update to 16.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
2022-12-13 00:07:22 +01:00
5167881a60
gnu: python-biopython: Update to 1.80.
...
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
2022-12-13 00:07:22 +01:00
2c8a53cb6b
gnu: bioperl-minimal: Remove trailing #T from build phase.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal)[arguments]: Remove
trailing #T from build phase.
2022-12-12 14:37:03 +01:00
fd44d489b5
gnu: python-biom-format: Update to 2.1.12.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12.
[arguments]: Remove "relax" phase; update "disable-broken-tests" phase.
[propagated-inputs]: Add python-scikit-bio.
2022-12-02 21:46:36 +01:00
b93e21a213
gnu: Add python-scikit-bio.
...
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
2022-12-02 21:46:36 +01:00
62da3f9837
gnu: python-pairtools: Update to 1.0.2.
...
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2.
[source]: Update Github URL.
[arguments]: Update patch in "fix-references" phase.
[native-inputs]: Remove python-nose.
[inputs]: Remove.
[propagated-inputs]: Add python-bioframe, python-pandas, python-pysam,
python-pyyaml, and python-scipy.
[home-page]: Update.
2022-12-02 21:46:36 +01:00
089b2e4f65
gnu: python-pairtools: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests
conditionally.
2022-12-02 21:46:36 +01:00
631ea9a411
gnu: python-pybedtools: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use
pyproject-build-system.
[arguments]: Import (guix build pyproject-build-system).
2022-12-02 21:46:36 +01:00
a268b1ba91
gnu: python-htsget: Update to 0.2.6.
...
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6.
[build-system]: Use pyproject-build-system.
2022-12-02 21:46:35 +01:00
16ecce39d2
gnu: python-cellbender: Update to 0.2.2.
...
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2.
[build-system]: Use pyproject-build-system.
2022-12-02 21:46:35 +01:00
62ddd3bc80
gnu: Add python-fanc.
...
* gnu/packages/bioinformatics.scm (python-fanc): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02 17:43:20 +01:00
ee069ec651
gnu: Add python-genomic-regions.
...
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02 17:20:54 +01:00
b095dac8e0
gnu: Add r-btools.
...
* gnu/packages/bioinformatics.scm (r-btools): New variable.
2022-11-25 11:17:56 +01:00
ebde19092f
gnu: r-circus: Update to 0.1.7.
...
* gnu/packages/bioinformatics.scm (r-circus): Update to 0.1.7.
[properties]: Add upstream-name property.
[propagated-inputs]: Add r-biocgenerics, r-genomeinfodb, and r-rtracklayer.
2022-11-17 15:00:49 +01:00
02db3f51b7
gnu: Add r-disgenet2r.
...
* gnu/packages/bioinformatics.scm (r-disgenet2r): New variable.
2022-11-15 11:03:24 +01:00
b4e3e02fd1
gnu: Add r-pando.
...
* gnu/packages/bioinformatics.scm (r-pando): New variable.
2022-11-09 09:55:14 +01:00
49e1a3a04b
gnu: Add python-cooltools.
...
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
2022-11-04 13:50:20 +01:00
14cbaac69c
gnu: Add python-bioframe.
...
X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
2022-11-04 13:39:12 +01:00
1b0fea29a0
gnu: r-dyngen: Update to 1.0.5.
...
* gnu/packages/bioinformatics.scm (r-dyngen): Update to 1.0.5.
2022-11-04 10:01:05 +01:00
15ff5eebb6
gnu: Fix various lint issues in synopsis and descriptions.
...
* gnu/packages/android.scm (etc1tool)[synopsis]: Drop trailing period.
* gnu/packages/bioinformatics.scm (mudskipper)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-async-log-attributes-1)[synopsis]: Likewise.
(rust-atomic-polyfill-1)[synopsis]: Likewise.
(rust-modifier-0.1)[synopsis]: Likewise.
(rust-openssl-macros-0.1)[synopsis]: Likewise.
(rust-syn-mid-0.5)[synopsis]: Likewise.
(rust-toml-edit-0.14)[synopsis]: Likewise.
(rust-valuable-derive-0.1)[synopsis]: Likewise.
(rust-inflections-1)[synopsis]: Likewise.
* gnu/packages/databases.scm (python-databases)[synopsis]: Likewise.
* gnu/packages/games.scm (liquidwar6)[synopsis]: Likewise.
* gnu/packages/golang.scm (go-golang.org-x-sync-errgroup)[synopsis]: Likewise.
* gnu/packages/guile-xyz.scm (guile-config)[synopsis]: Likewise.
* gnu/packages/haskell-web.scm (ghc-hxt-xpath)[synopsis]: Likewise.
* gnu/packages/haskell-xyz.scm (ghc-string-qq)[synopsis]: Likewise.
* gnu/packages/machine-learning.scm (python-lap)[synopsis]: Likewise.
(python-pyro-api)[synopsis]: Likewise.
* gnu/packages/messaging.scm (python-librecaptcha)[synopsis]: Likewise.
* gnu/packages/python-check.scm (python-pytest-cram)[synopsis]: Likewise.
* gnu/packages/python-web.scm (python-jschema-to-python)[synopsis]: Likewise.
(python-sarif-om)[synopsis]: Likewise.
(python-socksio)[synopsis]: Likewise.
(python-msrest)[synopsis]: Likewise.
* gnu/packages/tor.scm (torsocks)[synopsis]: Likewise.
* gnu/packages/cran.scm (r-rlist)[synopsis]: Remove leading article.
* gnu/packages/crates-io.scm (rust-clippy-lints-0.0.153)[synopsis]: Likewise.
(rust-simplelog-0.11)[synopsis]: Likewise.
* gnu/packages/samba.scm (wsdd)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-spki-0.4)[synopsis]: Remove trailing
whitespace.
* gnu/packages/golang.scm (go-github-com-mattn-go-zglob)[description]: Remove
leading whitespace.
* gnu/packages/haskell-check.scm (ghc-crypto-cipher-tests)[description]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-ctype)[synopsis]: Remove trailing
whitespace.
* gnu/packages/mpi.scm (openmpi-thread-multiple)[description]: Remove leading
whitespace.
* gnu/packages/node-xyz.scm (node-string-decoder)[synopsis]: Remove trailing
whitespace.
2022-10-31 18:13:48 -07:00
75b24abf09
gnu: flair: Update to 1.6.4.
...
* gnu/packages/bioinformatics.scm (flair): Update to 1.6.4.
[propagated-inputs]: Add python-numpy and python-scipy.
2022-10-28 15:00:21 +02:00
bb4f24b3ae
gnu: flair: Set R_HOME.
...
* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
2022-10-28 15:00:21 +02:00
28950ed561
gnu: flair: Add missing R package.
...
* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
2022-10-28 15:00:20 +02:00
176a501360
gnu: flair: Add missing R packages.
...
* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2.
[inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman,
and r-rlang.
[arguments]: Add phase "wrap-executable".
2022-10-27 18:21:22 +02:00
fe7b421d05
gnu: Add python-multivelo.
...
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
2022-10-27 15:15:19 +02:00
358a1fdf7b
gnu: Add r-seuratwrappers.
...
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
2022-10-27 15:03:21 +02:00
a2e4e3489b
gnu: Various typo fixes.
...
* gnu/packages/emacs-xyz.scm (emacs-popup-kill-ring)[description]: Fix very
sneaky "This packages" variant. Thanks to nckhexen!
* gnu/packages/bioinformatics.scm (r-icellnet)[description]: Fix use of
"allows to".
* gnu/packages/check.scm (python-pytest-freezegun)[description]: Ditto.
* gnu/packages/linux.scm (tp-smapi-module)[description]: Ditto.
* gnu/packages/mail.scm (procmail): Ditto.
* gnu/packages/maths.scm (maxima): Ditto.
* gnu/packages/samba.scm (wsdd)[description]: Ditto.
* gnu/packages/ssh.scm (openssh): Ditto.
2022-10-24 17:35:19 -07:00
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.
...
* 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.
...
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.
...
* gnu/packages/bioinformatics.scm (megahit): New variable.
2022-10-05 17:59:04 +02:00
be1d561f1a
gnu: Add cd-hit-auxtools.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (centrifuge): New variable.
2022-09-30 16:59:18 +02:00
1ee2d117d8
gnu: blast+: Build reproducibly.
...
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
990a4822f1
Merge branch 'staging' into core-updates
...
Conflicts resolved in:
gnu/local.mk
gnu/packages/cran.scm
gnu/packages/gnome.scm
gnu/packages/gtk.scm
gnu/packages/icu4c.scm
gnu/packages/java.scm
gnu/packages/machine-learning.scm
gnu/packages/tex.scm
2022-09-27 15:59:30 -04:00
c1716ab6ec
gnu: Add r-compgenomrdata.
...
* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
2022-09-26 17:21:57 +02:00
cbe8391d7c
gnu: Add mudskipper.
...
* gnu/packages/bioinformatics.scm (mudskipper): New variable.
2022-09-23 00:21:40 +02:00
1a1ff7ed8f
gnu: python-cooler: Skip broken test.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
2022-09-21 11:09:46 +02:00
a7f6392caa
gnu: Add r-skitools.
...
* gnu/packages/bioinformatics.scm (r-skitools): New variable.
2022-09-21 11:09:46 +02:00
af663c9e48
gnu: Add r-gchain.
...
* gnu/packages/bioinformatics.scm (r-gchain): New variable.
2022-09-21 11:09:46 +02:00
6ad4d74aca
gnu: Add r-gtrack.
...
* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
2022-09-21 11:09:46 +02:00
29634a4ce3
gnu: Add r-bamutils.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Replace
python-setuptools with python-setuptools-for-tensorflow.
2022-09-20 17:02:34 +02:00
a91cf65a7e
gnu: Python: Update to 3.10.7.
...
* gnu/packages/python.scm (python-3.9): Rename to ...
(python-3.10): ... this. Update to 3.10.7.
[source](patches): Remove 'python-3-no-static-libs.patch' in favor of ...
[arguments]: Add #:configure-flags.
(python-3): Refer to PYTHON-3.10.
* gnu/packages/patches/python-3-fix-tests.patch: Refresh.
* gnu/packages/patches/python-3-no-static-lib.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/version-control.scm (mercurial)[native-search-paths]: Adjust
Python version.
* gnu/packages/admin.scm (ansible)[native-search-paths]: Likewise.
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Replace hard-coded
python3.9 paths with python3.10.
* gnu/packages/cran.scm (r-torch)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (liblantern)[arguments]: Likewise.
2022-09-18 17:06:05 +02:00
7e0f2728a4
Merge branch 'staging' into core-updates
2022-09-16 19:11:43 +02:00
b736af1824
gnu: catch-framework2: Rename variable to catch2.
...
Automated with:
git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i
2022-09-15 20:15:56 -04:00
4920f6e634
Merge branch 'staging' into core-updates
...
Conflicts resolved in:
gnu/local.mk
gnu/packages/cmake.scm
gnu/packages/glib.scm
gnu/packages/gnome.scm
gnu/packages/gtk.scm
gnu/packages/sdl.scm
pango-next, vala-next and librsvg-bootstrap were removed in the process.
2022-09-15 11:43:21 -04:00
a7af25ad31
gnu: kraken2: Update to 2.1.2.
...
* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2.
2022-09-13 17:35:38 +02:00
1d526f5035
Merge branch 'staging' into core-updates
2022-09-10 17:30:17 +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
884548b476
Merge branch 'staging' into core-updates
2022-09-08 21:12:52 +02:00
453e7dd8c4
gnu: tombo: Disable tests.
...
* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
2022-09-07 17:36:42 +02:00
58863b93b0
Merge branch 'staging' into core-updates
2022-09-01 23:26:57 +02:00
36445e4d96
gnu: pigx-bsseq: Update to 0.1.8.
...
* 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.
...
* 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
ad384816fe
Merge branch 'staging' into core-updates
2022-08-27 17:10:55 +02:00
d26b29d263
gnu: Add flair.
...
* gnu/packages/bioinformatics.scm (flair): New variable.
2022-08-23 13:30:52 +02:00
8d42898572
gnu: python-mappy: Update to 2.24.
...
* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
2022-08-23 13:29:17 +02:00
f3a7d43281
gnu: Add r-kbet.
...
* gnu/packages/bioinformatics.scm (r-kbet): New variable.
2022-08-18 12:21:07 +02:00
8aab1f7c73
gnu: Add go-github-com-biogo-biogo.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
2022-08-16 16:09:54 +02:00
872e17ddc1
gnu: Add stpipeline.
...
* gnu/packages/bioinformatics.scm (stpipeline): New variable.
2022-08-16 15:22:07 +02:00
9c2400c282
gnu: Add python-taggd.
...
* gnu/packages/bioinformatics.scm (python-taggd): New variable.
2022-08-16 15:22:07 +02:00
752be79bf3
gnu: htseq: Update to 2.0.2.
...
* 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
...
* 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
77eb3008e3
Merge branch 'staging' into core-updates
2022-08-11 23:36:10 +02:00
26bdefd172
gnu: Add r-liana.
...
* gnu/packages/bioinformatics.scm (r-liana): New variable.
2022-08-10 15:44:28 +02:00
fd4b8e9873
gnu: Add r-omnipathr/devel.
...
* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
2022-08-10 15:44:28 +02:00
0b55b036c1
gnu: cereal: Update to 1.3.2.
...
* gnu/packages/serialization.scm (cereal): Update to 1.3.2.
[arguments]: Use G-expression.
(cereal-1.3.0): New variable.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Change from CEREAL to
CEREAL-1.3.0.
* gnu/packages/engineering.scm (prusa-slicer)[inputs]: Likewise.
2022-08-10 00:28:59 +02:00
ec6499aad2
gnu: Add phyml.
...
* gnu/packages/bioinformatics.scm (phyml): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-08 12:38:41 +02:00
03858a7908
gnu: Add python-scanorama.
...
* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
2022-08-02 14:37:38 +02:00
c69c2c1c4d
gnu: python-intervaltree: Update to 3.1.0.
...
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
2022-08-02 14:37:38 +02:00
f1b9ae8c20
gnu: python-bbknn: Update to 1.5.1.
...
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1.
[propagated-inputs]: Add python-pandas.
2022-08-01 17:46:21 +02:00
8d7a721400
gnu: Add r-millefy.
...
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
2022-08-01 15:14:47 +02:00
dc3ad40c6b
gnu: python-bbknn: Set NUMBA_CACHE_DIR.
...
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'set-numba-cache-dir.
2022-08-01 12:46:19 +02:00
1ef04fb228
gnu: qtsvg: Rename variable to qtsvg-5.
...
This is in preparation of the qtsvg update to version 6.
This change was automated via the following command:
git grep -l '\bqtsvg\b' | xargs sed 's/qtsvg/qtsvg-5/g' -i
2022-07-31 21:55:43 -04:00
e6bdd94c38
gnu: plink-ng: Fix building on other architectures.
...
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to add simde includes to CFLAGS.
[native-inputs]: Add simde.
2022-07-28 23:47:40 +03:00
99d1122f8b
gnu: plink-ng: Update to 2.00a3.3.
...
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
2022-07-28 22:55:07 +03:00
9044b086dd
Merge branch 'staging' into core-updates
2022-07-22 01:09:14 +02:00
d84bedd830
gnu: Add python-cellbender.
...
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
2022-07-09 10:37:22 +02:00
6211ecfec8
gnu: Add hh-suite.
...
* gnu/packages/bioinformatics.scm (hh-suite): New variable.
2022-07-06 14:00:21 +02:00
a0125732ef
gnu: Add r-sccustomize.
...
* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
2022-07-04 13:48:58 +02:00
4d77072c56
gnu: libsbml: Use regular check.
...
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14
with check.
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-07-02 11:28:28 +02:00
81cf674a5d
gnu: Add python-ikarus.
...
* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
2022-07-01 14:54:26 +02:00
8655a71445
Merge branch master into core-updates
2022-06-22 18:48:00 +02:00
f700223c3b
gnu: Add pyscenic.
...
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
2022-06-16 15:20:59 +02:00
3535d8dc5a
gnu: Add python-arboreto.
...
* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
2022-06-16 15:20:59 +02:00
fbe5707b73
gnu: Add python-ctxcore.
...
* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
2022-06-16 15:20:59 +02:00
8c3e9da13a
Merge branch 'master' into core-updates
2022-06-08 14:46:24 +02:00
964cdd57fa
gnu: discrover: Use reproducible timestamps.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add
'set-force-source-date phase.
2022-06-06 15:08:18 -07:00
b483ef1a88
gnu: python-pybedtools: Update to 0.9.0.
...
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0.
[description]: Update to satisfy guix lint.
[license]: Update to expat and lgpl2.1+.
2022-06-09 23:10:15 -07:00
b540e5e6bb
gnu: pigx-scrnaseq: Update to 1.1.9.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
2022-06-01 12:57:22 +02:00
93c97bfffb
gnu: pigx-bsseq: Update to 0.1.7.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove automake and autoconf.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2022-06-01 12:41:59 +02:00
6e54ce9ca9
gnu: pigx-chipseq: Update to 0.1.0.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2022-06-01 12:19:48 +02:00
cd95d7ddd1
gnu: pigx-rnaseq: Update to 0.1.0.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
2022-06-01 11:07:27 +02:00
0aae2f7f01
gnu: pigx-rnaseq: Update to 0.0.21.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
2022-06-01 10:46:00 +02:00
0c26c8da9d
gnu: pigx-rnaseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
2022-06-01 10:46:00 +02:00
b279e778ab
gnu: Add sylamer.
...
* gnu/packages/bioinformatics.scm (sylamer): New variable.
2022-06-01 00:17:05 +02:00
c35e508b4a
gnu: Remove python2-biopython.
...
* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
2022-05-31 14:54:17 -04:00
ad030a0b7d
gnu: Remove pplacer-scripts.
...
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
2022-05-31 14:54:17 -04:00
d397cb6207
gnu: Remove pplacer.
...
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
2022-05-31 14:54:16 -04:00
026fca8b5b
gnu: Remove python2-checkm-genome.
...
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
2022-05-31 14:54:15 -04:00
4d7bb37981
gnu: Remove fraggenescan.
...
* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
2022-05-31 14:54:02 -04:00
6792b0b6cd
gnu: Remove python2-pysam.
...
* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
2022-05-31 14:53:35 -04:00
955e7d628d
gnu: Remove find-circ.
...
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
2022-05-31 14:53:34 -04:00
a5e29cd838
gnu: Remove gess.
...
* gnu/packages/bioinformatics.scm (gess): Delete variable.
2022-05-31 14:53:34 -04:00
c30ab2c0b4
gnu: Remove pyicoteo.
...
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
2022-05-31 14:52:19 -04:00
ba09192168
gnu: Remove python2-pbcore.
...
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31 14:52:19 -04:00
8287979669
gnu: Remove python2-pyfaidx.
...
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31 14:52:18 -04:00
850bd0c329
gnu: Remove python2-screed.
...
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31 14:52:18 -04:00
a94bc7798a
gnu: Remove miso.
...
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31 14:52:18 -04:00
23e133a907
gnu: Remove python2-warpedlmm.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31 14:52:18 -04:00
bb35b50adc
gnu: Remove poretools.
...
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31 14:52:18 -04:00
bcdd45be6f
gnu: Remove python2-dendropy.
...
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31 14:52:17 -04:00
d2c971e67b
gnu: Remove bamm.
...
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31 14:52:17 -04:00
1010c05800
gnu: Remove python2-pybedtools.
...
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31 14:52:17 -04:00
725b562962
gnu: Remove python2-htseq.
...
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31 14:52:17 -04:00
8bcb07d089
gnu: Remove pepr.
...
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31 14:52:17 -04:00
3d63c5f1ba
gnu: tetoolkit: Update to 2.2.1b.
...
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam.
[home-page]: Update URL.
2022-05-31 14:52:16 -04:00
d29d50a556
gnu: Remove python2-pybigwig.
...
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31 14:52:16 -04:00
98c4f97d18
gnu: Remove ribodiff.
...
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31 14:52:16 -04:00
9f4c958d62
gnu: Remove grit.
...
* gnu/packages/bioinformatics.scm (grit): Delete variable.
2022-05-31 14:52:16 -04:00
7963e12568
gnu: Remove python2-fastalite.
...
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
2022-05-31 14:52:16 -04:00
0bcd28e58c
gnu: python-scanpy: Update to 1.9.1.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
2022-05-30 23:09:46 +02:00
cb115ba722
gnu: pigx-sars-cov-2: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
2022-05-29 00:39:19 +02:00
df3e5cfa05
gnu: pigx-bsseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
2022-05-29 00:34:29 +02:00
b64f4a1245
gnu: pigx-scrnaseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
2022-05-29 00:29:19 +02:00
add551f651
gnu: pigx-chipseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
2022-05-29 00:18:48 +02:00
b015a15c57
gnu: Fix all this damn packages.
...
* gnu/packages/bioinformatics.scm (r-icellnet)[description]:
Fix ‘this packages’ typo.
* gnu/packages/cran.scm (r-add2ggplot)[description]: Likewise.
* gnu/packages/crates-io.scm (rust-const-oid-0.6, rust-pem-rfc7468-0.2)
(rust-scrypt-0.8)[description]: Likewise.
2022-05-22 02:00:00 +02:00
dab819d5c4
Move (gnu platform) and (gnu platforms ...) to guix/.
...
* gnu/platform.scm:
* gnu/platforms/arm.scm:
* gnu/platforms/hurd.scm:
* gnu/platforms/mips.scm:
* gnu/platforms/powerpc.scm:
* gnu/platforms/riscv.scm:
* gnu/platforms/s390.scm:
* gnu/platforms/x86.scm: Move to guix/.
* Makefile.am:
* doc/guix.texi (Porting to a New Platform):
* etc/release-manifest.scm:
* gnu/ci.scm:
* gnu/image.scm:
* gnu/local.mk:
* gnu/packages/bioinformatics.scm:
* gnu/packages/bootstrap.scm:
* gnu/packages/cross-base.scm:
* gnu/packages/instrumentation.scm:
* gnu/packages/linux.scm:
* gnu/system/image.scm:
* gnu/system/images/hurd.scm:
* gnu/system/images/novena.scm:
* gnu/system/images/pine64.scm:
* gnu/system/images/pinebook-pro.scm:
* gnu/system/images/rock64.scm:
* guix/scripts/build.scm:
* guix/scripts/system.scm:
* guix/self.scm: Update (gnu platform...) to (guix platform...).
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-05-25 09:27:25 +02:00
b55310603f
linux: Remove system->linux-architecture procedure.
...
* gnu/packages/linux.scm (system->linux-architecture): Remove it.
(make-linux-libre-headers*, make-linux-libre*): Adapt them.
* guix/build-system/linux-module.scm (system->arch): Adapt it.
* gnu/packages/instrumentation.scm (uftrace): Ditto.
* gnu/packages/cross-base.scm (cross-kernel-headers): Ditto.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Ditto.
* doc/guix.texi (Porting to a new platform): Update it.
2022-05-22 15:15:33 +02:00
a1a55e5b60
gnu: fastahack: Wrap long line.
...
* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
2022-05-12 12:59:18 +05:30
aaa981f7c5
gnu: cwltool: Do not propagate inputs.
...
* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ...
[inputs]: ... here.
2022-05-11 10:52:45 +05:30
8d25887d87
gnu: vcflib: Set absolute path to pkg-config.
...
Setting the absolute path to pkg-config is required to support
cross-compilation.
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Set
PKG_CONFIG_EXECUTABLE in #:configure-flags.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:19:43 +03:00
9047a31152
gnu: vcflib: Find submodule sources in native-inputs during cross-compilation.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In the
unpack-submodule-sources phase, look for submodule sources in both inputs and
native-inputs.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:19:39 +03:00
9a68c07507
gnu: vcflib: Use G-expressions.
...
* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using
G-expressions.
[arguments]: Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:19:03 +03:00
9258576eea
gnu: fastahack: Use compiler specific to the build target.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Set CXX in
#:make-flags. In the build-dynamic phase, use cxx-for-target instead of g++.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:18:09 +03:00
713dadf47e
gnu: fastahack: Use G-expressions.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Rewrite
using G-expressions. Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:17:51 +03:00
086c7c143c
gnu: tabixpp: Fix cross-compilation.
...
tabixpp links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and
xz should be listed in inputs even though they are already present implicitly
in native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (tabixpp)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:17:25 +03:00
cbda00c499
gnu: tabixpp: Use build tools specific to the target.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Set CC and CXX in
#:make-flags. In the build-libraries phase, use cxx-for-target instead of g++
and ar-for-target instead of ar.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:15:12 +03:00
a990547952
gnu: tabixpp: Use #:make-flags.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Do not override the
build phase. Move the required make arguments to #:make-flags. Add
build-libraries phase.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:14:18 +03:00
ff1fd3b012
gnu: tabixpp: Use G-expressions.
...
* gnu/packages/bioinformatics.scm (tabixpp)[source]: Reindent.
[arguments]: Use search-input-file and search-input-directory.
[source, arguments]: Rewrite using G-expressions. Do not return #t from
snippets and custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09 11:13:40 +03:00
6f5cbac67d
gnu: pigx-sars-cov-2: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
2022-05-06 15:34:31 +02:00
f550c0ccb0
gnu: Add pigx-sars-cov-2.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable.
(pigx-sars-cov2-ww): Deprecate this package in favor of the former.
2022-05-06 15:34:31 +02:00
39d6c13fda
gnu: python-hic2cool: Fix build.
...
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
2022-05-02 17:33:31 +02:00
b1dd32d8e3
gnu: htslib-for-stringtie: Inherit from htslib-1.12.
...
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
2022-05-02 14:35:26 +02:00
5caad9f252
gnu: python-cooler: Use more recent cytoolz.
...
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
2022-05-02 13:33:16 +02:00
33fe027f91
gnu: Add r-giotto.
...
* gnu/packages/bioinformatics.scm (r-giotto): New variable.
2022-04-26 09:48:14 +02:00
ffb616b69d
gnu: vcflib: Update to 1.0.3.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3.
[source]: Remove trailing #t.
[arguments]: Remove trailing #t from phases.
2022-04-19 21:56:50 +03:00
7034746e15
gnu: scregseg: Remove cythonized file.
...
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
2022-04-14 22:55:33 +03:00
c8a6e4abbc
gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).
...
* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
2022-04-14 13:35:22 +02:00
6413d0898b
gnu: Add r-copykat.
...
* gnu/packages/bioinformatics.scm (r-copykat): New variable.
2022-04-11 16:11:45 +02:00
96a132809f
gnu: smithwaterman: Fix cross-compiling.
...
The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences.
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More
closely match the 'ar' and 'ld' commands when substituting them.
2022-04-10 20:49:33 +03:00
e3e3381fdb
gnu: Add r-rnaseqdtu.
...
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-06 11:43:46 +02:00
df2dc0c416
gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.
...
This is needed since the update of python-loompy.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename
'set-PYTHONPATH to 'set-additional-environment-variables and set
NUMBA_CACHE_DIR.
2022-04-05 18:40:48 +02:00
e721122069
gnu: pigx-scrnaseq: Use new inputs style.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
2022-04-05 18:40:48 +02:00
5d1c9fcdcf
gnu: pigx-scrnaseq: Update to 1.1.8.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
[patches]: Remove.
[native-inputs]: Remove.
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-04-05 18:40:48 +02:00
345f79b2cf
gnu: freebayes: Fix test suite.
...
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
2022-04-04 22:58:25 +03:00
c1fc65ecb6
gnu: smithwaterman: Use new style for phases.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
2022-04-04 22:45:37 +03:00
855c8d9d41
gnu: smithwaterman: Fix cross-compiling.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add
make-flag to use cxx-for-target. Adjust custom 'patch-source and
'build-dynamic phases to use cross toolchain binaries when cross
compiling. Remove trailing #t from phases.
2022-04-04 22:41:54 +03:00
05e68f31ba
gnu: python-velocyto: Set cache directory for Numba.
...
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
2022-03-31 16:02:21 +02:00
8f3dc994bb
gnu: wfmash: Enable test suite.
...
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
2022-03-31 16:29:34 +03:00
1ca9d9e194
gnu: Add wfmash.
...
* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:53 +03:00
7d331dd203
gnu: htslib: Add bzip2 and xz to inputs.
...
htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:52 +03:00
a69a44bf59
gnu: python-loompy: Update to 3.0.7.
...
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
2022-03-31 14:37:58 +02:00
591007f7d1
gnu: r-signac: Update to 1.6.0-2.458e647.
...
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 17:40:17 +02:00
977a33139e
gnu: plink-ng: Update to 2.00a3-20220315.
...
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
2022-03-29 15:33:55 +02:00
d710f01957
gnu: Add r-cytobackbone.
...
* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 14:03:44 +02:00
6d5964e804
gnu: pigx-sars-cov2-ww: Update to 0.0.5.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
847acc3206
gnu: pigx-rnaseq: Update to 0.0.20.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
a9429c8f22
Merge branch 'staging' into core-updates.
2022-03-21 23:39:43 -04:00
ca588fdfde
gnu: Add r-scopeloomr.
...
* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
2022-03-09 11:35:59 +01:00
e5dbda5abc
gnu: texlive-latex-pgf: Rename to "texlive-pgf".
...
Suggested by Ricardo Wurmus.
* gnu/packages/tex.scm (texlive-latex-pgf): Rename to...
(texlive-pgf): ... this. Change 'name' accordingly.
(texlive-latex-pgf): Define as deprecated.
(texlive-beamer)[propagated-inputs]: Use the new name.
(texlive-todonotes)[propagated-inputs]: Likewise.
(texlive-adjustbox)[propagated-inputs]: Likewise.
(texlive-tcolorbox)[propagated-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
2022-03-02 19:26:16 +01:00
a6867b2d98
gnu: minimap2: Update to 2.24.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
2022-02-27 11:42:30 +02:00
3fb78caa55
gnu: Add r-dyngen.
...
* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
2022-02-22 18:48:30 +01:00
d293162615
gnu: Add texlive-pgf.
...
* gnu/packages/tex.scm (texlive-pgf): New variable.
(texlive-latex-pgf): Deprecate variable.
(texlive-beamer):
(texlive-latex-xkeyval):
(texlive-todonotes):
(texlive-adjustbox):
(texlive-tcolorbox):
* gnu/packages/bioinformatics.scm (discrover): Use new variable.
2022-02-14 00:08:30 +01:00
970b7a949d
gnu: Add texlive-graphics.
...
* gnu/packages/tex.scm (texlive-graphics): New variable.
(texlive-latex-graphics): Deprecate variable.
(texlive-base):
(texlive-pstool):
(texlive-jadetex):
* gnu/packages/bioinformatics.scm (velvet):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-numpy-documentation):
(python-ipython-documentation):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/statistics.scm (r-with-tests): Use new variable.
2022-02-14 00:08:30 +01:00
Ricardo Wurmus
Navid Afkhami
Mădălin Ionel Patrașcu
Vagrant Cascadian
Hong.Li@mdc-berlin.de
Christopher Baines
Maxim Cournoyer
Marius Bakke
Efraim Flashner
Thiago Jung Bauermann
Ludovic Courtès
Vagrant Cascadian
Tobias Geerinckx-Rice
Josselin Poiret
Mathieu Othacehe
Arun Isaac
zimoun
Hong Li
Nicolas Goaziou