1838 commits

Author	SHA1	Message	Date
Ricardo Wurmus	3153ca9d5f	gnu: r-rhtslib: Fix build. ... * gnu/packages/bioinformatics.scm (r-rhtslib)[arguments]: Add "--no-staged-install" to configure flags.	2019-04-27 22:45:02 +02:00
Ricardo Wurmus	fc3ebc3023	gnu: r-ggbio: Fix build. ... * gnu/packages/bioinformatics.scm (r-ggbio)[arguments]: Add build phase to patch out typo.	2019-04-27 20:45:21 +02:00
Ricardo Wurmus	7f55904558	gnu: Add umi-tools. ... * gnu/packages/bioinformatics.scm (umi-tools): New variable.	2019-04-26 21:00:37 +02:00
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	c2f6f4e500	gnu: Add python2-checkm-genome. ... * gnu/packages/bioinformatics.scm (python2-checkm-genome): New variable.	2019-04-11 17:54:57 +02:00
Ricardo Wurmus	36f4f1e297	gnu: Add pplacer. ... * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.	2019-04-11 17:18:08 +02:00
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Efraim Flashner	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
Ricardo Wurmus	e9d4409bab	gnu: Add python-bbknn. ... * gnu/packages/bioinformatics.scm (python-bbknn): New variable.	2019-03-29 03:55:45 +01:00
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	fdfaba9032	gnu: Add starlong. ... * gnu/packages/bioinformatics.scm (starlong): New variable.	2019-03-22 16:17:01 +01:00
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	35f9c6628f	gnu: Add adapterremoval. ... * gnu/packages/bioinformatics.scm (adapterremoval): New variable.	2019-03-20 12:19:55 +01:00
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	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
Ricardo Wurmus	6e42cef0ab	gnu: Add bbmap. ... * gnu/packages/bioinformatics.scm (bbmap): New variable.	2019-03-18 21:35:57 +01:00
Ricardo Wurmus	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
Ricardo Wurmus	19bd7f2e79	gnu: Add arriba. ... * gnu/packages/bioinformatics.scm (arriba): New variable.	2019-03-18 16:00:30 +01:00
Ricardo Wurmus	f88bdc5ff9	gnu: Add blasr. ... * gnu/packages/bioinformatics.scm (blasr): New variable.	2019-03-18 14:47:49 +01:00