296da6e624
gnu: r-seurat: Update to 3.0.0.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.0.
[propagated-inputs]: Remove r-dosnow, r-dplyr, r-dtw, r-foreach, r-fpc,
r-gplots, r-hdf5r, r-hmisc, r-httr, r-lars, r-mixtools, r-reshape2, and
r-tidyr; add r-future, r-future-apply, r-ggrepel, r-kernsmooth, r-rlang,
r-rsvd, r-scales, and r-sctransform.
2019-04-19 15:38:47 +02:00
c4a50a8a47
gnu: r-genomicfeatures: Update to 1.34.8.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.8.
2019-04-11 23:37:19 +02:00
c2f6f4e500
gnu: Add python2-checkm-genome.
...
* gnu/packages/bioinformatics.scm (python2-checkm-genome): New variable.
2019-04-11 17:54:57 +02:00
36f4f1e297
gnu: Add pplacer.
...
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
2019-04-11 17:18:08 +02:00
f613f9ae26
gnu: r-ldblock: Update to 1.12.1.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.1.
2019-04-06 23:13:26 +02:00
8f30d38238
gnu: r-ensembldb: Update to 2.6.8.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.8.
2019-04-06 23:13:26 +02:00
83546785b2
gnu: r-rcas: Add upstream name.
...
* gnu/packages/bioinformatics.scm (r-rcas)[properties]: Add upstream name.
2019-04-03 17:42:18 +02:00
cbe40b8b24
gnu: pigx-scrnaseq: Use older loompy.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
python-loompy with python-loompy-for-pigx-scrnaseq.
2019-04-02 16:11:23 +02:00
dc112a0fe2
gnu: Add python-loompy-for-pigx-scrnaseq.
...
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): New variable.
2019-04-02 16:11:12 +02:00
82cc117450
gnu: pigx-chipseq: Update to 0.0.40.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.40.
2019-04-02 15:53:23 +02:00
b4a33870f6
gnu: python-scanpy: Add python-louvain to inputs.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Sort
inputs and add python-louvain.
[arguments]: Do not delete test that depends on louvain.
2019-04-02 15:11:45 +02:00
36a4366d79
gnu: Fix descriptions to not use quotes.
...
* gnu/packages/admin.scm (wpa-supplicant-minimal, mingetty, di),
* gnu/packages/audio.scm (fil-plugins),
* gnu/packages/base.scm (make-ld-wrapper, make-glibc-locales),
* gnu/packages/bioinformatics.scm (r-samtools),
* gnu/packages/chez.scm (chez-mit),
* gnu/packages/commencement.scm (make-gcc-toolchain),
* gnu/packages/compression.scm (fastjar),
* gnu/packages/cran.scm (r-maps, r-rcpp),
* gnu/packages/databases.scm (sparql-query),
* gnu/packages/dunst.scm (dunst),
* gnu/packages/ftp.scm (ncftp),
* gnu/packages/gl.scm (freeglut),
* gnu/packages/haskell-check.scm (ghc-tasty-golden),
* gnu/packages/haskell.scm (ghc-case-insensitive, ghc-text,
ghc-haskell-src, ghc-syb, ghc-deepseq-generics, ghc-network-uri,
ghc-rerebase, ghc-zlib),
* gnu/packages/image.scm (jbig2dec),
* gnu/packages/kde-frameworks.scm (kinit, karchive),
* gnu/packages/linux.scm (wireless-tools, perf, module-init-tools, kbd),
* gnu/packages/lirc.scm (lirc),
* gnu/packages/lisp.scm (uglify-js),
* gnu/packages/mate.scm (mate-netbook),
* gnu/packages/microcom.scm (microcom),
* gnu/packages/music.scm (bristol),
* gnu/packages/networking.scm (perl-geo-ip),
* gnu/packages/patchutils.scm (patches),
* gnu/packages/perl-check.scm (perl-test-more-utf8),
* gnu/packages/perl.scm (perl-log-report-optional, perl-file-which,
perl-io-tty, perl-log-any, perl-digest-sha1, perl-class-load,
perl-regexp-common, perl-module-pluggable, perl-class-modifier),
* gnu/packages/python-xyz.scm (python-backports-abc, python-natsort),
* gnu/packages/samba.scm (iniparser),
* gnu/packages/search.scm (mlocate),
* gnu/packages/spice.scm (spice),
* gnu/packages/statistics.scm (r-dt, r-lubridate, r-estimability,
r-commonmark, r-digest, r-viridislite, r-stringr),
* gnu/packages/tex.scm (texlive-latex-changebar),
* gnu/packages/version-control.scm (subversion),
* gnu/packages/w3m.scm (w3m),
* gnu/packages/web.scm (perl-http-parser,
perl-plack-middleware-reverseproxy),
* gnu/packages/xorg.scm (xkeyboard-config, mkfontdir, xcursor-theme,
mkfontscale, xinit, font-alias)[description]: Use @code instead of quotes.
2019-03-31 20:51:10 +03:00
e9d4409bab
gnu: Add python-bbknn.
...
* gnu/packages/bioinformatics.scm (python-bbknn): New variable.
2019-03-29 03:55:45 +01:00
58d8225ddb
gnu: trim-galore: Add pigz.
...
* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz.
[arguments]: Embed reference to pigz.
2019-03-27 11:32:08 +01:00
5f1e31094d
gnu: trim-galore: Fix test for Python.
...
* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace
"configure" phase to skip ill-advised test for Python.
2019-03-27 11:28:38 +01:00
dfe420ee46
gnu: r-rhdf5lib: Update to 1.4.3.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.
2019-03-27 09:33:50 +01:00
3b6c77445b
gnu: r-genomicfeatures: Update to 1.34.7.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.
2019-03-27 09:33:50 +01:00
28d32817d8
gnu: python-scanpy: Update to 1.4.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.
[source]: Fetch from git.
[arguments]: Disable broken tests.
[native-inputs]: Add python-pytest.
[home-page]: Use HTTPS.
2019-03-26 18:06:35 +01:00
fdc316f374
gnu: trim-galore: Update to 0.6.1.
...
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1.
[arguments]: Adjust patching.
2019-03-26 16:40:42 +01:00
9ac17c6242
gnu: cutadapt: Update to 2.1.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1.
[source]: Fetch from pypi.
[native-inputs]: Add python-setuptools-scm.
2019-03-26 16:40:42 +01:00
80eb01c776
gnu: r-gkmsvm: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here...
* gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.
2019-03-25 14:34:41 +01:00
c5a2b518ad
gnu: r-wgcna: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-wgcna): Move from here...
* gnu/packages/cran.scm (r-wgcna): ...to here.
2019-03-25 14:05:09 +01:00
72a216a9d0
gnu: r-optparse: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-optparse): Move from here...
* gnu/packages/cran.scm (r-optparse): ...to here.
2019-03-25 14:04:19 +01:00
0ef062b338
gnu: r-bookdown: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-bookdown): Move from here...
* gnu/packages/cran.scm (r-bookdown): ...to here.
2019-03-25 14:03:21 +01:00
469fb43891
gnu: r-sparql: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-sparql): Move from here...
* gnu/packages/cran.scm (r-sparql): ...to here.
2019-03-25 14:01:56 +01:00
c4d521ba2c
gnu: r-seqinr: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-seqinr): Move from here...
* gnu/packages/cran.scm (r-seqinr): ...to here.
2019-03-24 23:44:13 +01:00
49a48c496f
gnu: r-acsnminer: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-acsnminer): Move from here...
* gnu/packages/cran.scm (r-acsnminer): ...to here.
2019-03-24 23:44:13 +01:00
9ebb7f8181
gnu: r-phangorn: Update to 2.5.3.
...
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.3.
2019-03-24 20:36:51 +01:00
adfbda0fb0
gnu: r-gqtlstats: Update to 1.14.1.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.1.
2019-03-24 20:36:51 +01:00
7a73c247b2
gnu: r-rbgl: Update to 1.58.2.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.2.
2019-03-24 20:36:51 +01:00
fdfaba9032
gnu: Add starlong.
...
* gnu/packages/bioinformatics.scm (starlong): New variable.
2019-03-22 16:17:01 +01:00
c2b45ac578
gnu: r-diversitree: Update to 0.9-11.
...
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
2019-03-21 00:02:49 +01:00
db39269c89
gnu: r-maldiquant: Update to 1.19.2.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
2019-03-21 00:02:49 +01:00
28d0eb2565
gnu: r-diversitree: Fix typo.
...
* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo
in package labels.
2019-03-21 00:02:48 +01:00
933cc19684
gnu: r-annotationhub: Update to 2.14.5.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
2019-03-20 22:32:37 +01:00
e49d5d34ed
gnu: r-genomicfeatures: Update to 1.34.6.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
2019-03-20 22:32:32 +01:00
2b83d218d8
gnu: r-variantannotation: Update to 1.28.13.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
2019-03-20 22:32:25 +01:00
0adb6f207b
gnu: r-category: Update to 2.48.1.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
2019-03-20 22:32:17 +01:00
e014dc78f0
gnu: r-dexseq: Update to 1.28.3.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
2019-03-20 22:32:11 +01:00
35f9c6628f
gnu: Add adapterremoval.
...
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
2019-03-20 12:19:55 +01:00
c5542196d5
gnu: nanopolish: Use python-wrapper.
...
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with
"python-wrapper" as scripts require "python" executable.
2019-03-19 13:30:41 +01:00
7c1685e9d8
gnu: nanopolish: Remove bundled library sources.
...
* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove
bundled htslib sources.
2019-03-19 13:30:41 +01:00
9e1d9a0a46
gnu: python-biom-format: Fix build.
...
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove
generated C files.
[arguments]: Disable second broken test.
2019-03-18 23:46:27 +01:00
6e42cef0ab
gnu: Add bbmap.
...
* gnu/packages/bioinformatics.scm (bbmap): New variable.
2019-03-18 21:35:57 +01:00
ee4ca57809
gnu: blasr: Add home page.
...
Reported by Efraim Flashner <efraim@flashner.co.il> on IRC.
* gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
2019-03-18 16:02:30 +01:00
19bd7f2e79
gnu: Add arriba.
...
* gnu/packages/bioinformatics.scm (arriba): New variable.
2019-03-18 16:00:30 +01:00
f88bdc5ff9
gnu: Add blasr.
...
* gnu/packages/bioinformatics.scm (blasr): New variable.
2019-03-18 14:47:49 +01:00
6a6cd48cf0
gnu: Add blasr-libcpp.
...
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
2019-03-18 14:47:45 +01:00
55154c5f40
gnu: Add pbbam.
...
* gnu/packages/bioinformatics.scm (pbbam): New variable.
2019-03-18 14:47:26 +01:00
07c8b558e3
gnu: Add bwa-meth.
...
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
2019-03-15 11:36:56 +01:00
Ricardo Wurmus