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Author SHA1 Message Date
Ricardo Wurmus
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
Ricardo Wurmus
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
Navid Afkhami
b095dac8e0
gnu: Add r-btools. 
* gnu/packages/bioinformatics.scm (r-btools): New variable.
 2022-11-25 11:17:56 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
02db3f51b7
gnu: Add r-disgenet2r. 
* gnu/packages/bioinformatics.scm (r-disgenet2r): New variable.
 2022-11-15 11:03:24 +01:00
Mădălin Ionel Patrașcu
b4e3e02fd1
gnu: Add r-pando. 
* gnu/packages/bioinformatics.scm (r-pando): New variable.
 2022-11-09 09:55:14 +01:00
Mădălin Ionel Patrașcu
49e1a3a04b
gnu: Add python-cooltools. 
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
 2022-11-04 13:50:20 +01:00
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Vagrant Cascadian
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
Ricardo Wurmus
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
Ricardo Wurmus
bb4f24b3ae
gnu: flair: Set R_HOME. 
* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
28950ed561
gnu: flair: Add missing R package. 
* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
 2022-10-28 15:00:20 +02:00
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
fe7b421d05
gnu: Add python-multivelo. 
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
 2022-10-27 15:15:19 +02:00
Hong.Li@mdc-berlin.de
358a1fdf7b
gnu: Add r-seuratwrappers. 
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
 2022-10-27 15:03:21 +02:00
Vagrant Cascadian
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
Vagrant Cascadian
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
Ricardo Wurmus
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
Christopher Baines
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
Ricardo Wurmus
fd6cd9de86
gnu: Add megahit. 
* gnu/packages/bioinformatics.scm (megahit): New variable.
 2022-10-05 17:59:04 +02:00
Ricardo Wurmus
be1d561f1a
gnu: Add cd-hit-auxtools. 
* gnu/packages/bioinformatics.scm (cd-hit-auxtools): New variable.
 2022-10-05 14:28:24 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
729ce5fcf8
gnu: Add centrifuge. 
* gnu/packages/bioinformatics.scm (centrifuge): New variable.
 2022-09-30 16:59:18 +02:00
Ricardo Wurmus
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
Maxim Cournoyer
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
Ricardo Wurmus
c1716ab6ec
gnu: Add r-compgenomrdata. 
* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
 2022-09-26 17:21:57 +02:00
Ricardo Wurmus
cbe8391d7c
gnu: Add mudskipper. 
* gnu/packages/bioinformatics.scm (mudskipper): New variable.
 2022-09-23 00:21:40 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
d871080a41
gnu: Add r-chromunity. 
* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
a7f6392caa
gnu: Add r-skitools. 
* gnu/packages/bioinformatics.scm (r-skitools): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
af663c9e48
gnu: Add r-gchain. 
* gnu/packages/bioinformatics.scm (r-gchain): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
6ad4d74aca
gnu: Add r-gtrack. 
* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
 2022-09-21 11:09:46 +02:00
Ricardo Wurmus
29634a4ce3
gnu: Add r-bamutils. 
* gnu/packages/bioinformatics.scm (r-bamutils): New variable.
 2022-09-21 11:09:45 +02:00
Ricardo Wurmus
4bd64dde2b
gnu: Add r-gutils. 
* gnu/packages/bioinformatics.scm (r-gutils): New variable.
 2022-09-21 11:09:41 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Marius Bakke
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
Marius Bakke
7e0f2728a4
Merge branch 'staging' into core-updates 2022-09-16 19:11:43 +02:00
Maxim Cournoyer
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
Maxim Cournoyer
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
Ricardo Wurmus
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
Marius Bakke
1d526f5035
Merge branch 'staging' into core-updates 2022-09-10 17:30:17 +02:00
Christopher Baines
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
Marius Bakke
884548b476
Merge branch 'staging' into core-updates 2022-09-08 21:12:52 +02:00
Marius Bakke
453e7dd8c4
gnu: tombo: Disable tests. 
* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
 2022-09-07 17:36:42 +02:00
Marius Bakke
58863b93b0
Merge branch 'staging' into core-updates 2022-09-01 23:26:57 +02:00