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
fd4c7a098a
gnu: Add python-velocyto.
...
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
2019-03-13 22:48:53 +01:00
55a0a3c853
gnu: python-loompy: Update to 2.0.17.
...
* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
2019-03-13 22:48:52 +01:00
0b5d12ccdf
gnu: Add tetoolkit.
...
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
2019-03-13 15:14:10 +01:00
4dc2ecc279
gnu: r-qvalue: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-qvalue): Move from here...
* gnu/packages/bioconductor.scm (r-qvalue): ...to here.
2019-03-12 22:47:56 +01:00
8b6acb1f20
gnu: blast+: Update to 2.7.1.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1.
[inputs]: Add lmdb.
[source]: Remove obsolete patch.
* gnu/package/patches/blast+-fix-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2019-03-08 23:00:07 +01:00
183b6575e7
gnu: r-mzr: Update to 2.16.2.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2.
[inputs]: Replace "boost" with "boost-for-mysql".
2019-03-08 09:14:01 +01:00
6453d7aecc
gnu: r-gviz: Update to 1.26.5.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
2019-03-08 09:14:01 +01:00
101dcc29d3
gnu: r-ensembldb: Update to 2.6.7.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
2019-03-08 09:14:01 +01:00
d3713237c5
gnu: r-annotationhub: Update to 2.14.4.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
2019-03-08 09:14:01 +01:00
53e7f028ed
gnu: r-rhtslib: Update to 1.14.1.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
2019-03-08 09:14:01 +01:00
d86b9eca56
gnu: r-genomicfeatures: Update to 1.34.4.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
2019-03-08 09:14:01 +01:00
d493043daf
gnu: r-rtracklayer: Update to 1.42.2.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
2019-03-08 09:14:01 +01:00
57f40dc220
gnu: r-rsamtools: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
2019-03-08 09:14:00 +01:00
58209b1e21
gnu: r-biocparallel: Update to 1.16.6.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
2019-03-08 09:14:00 +01:00
cd43ae3fd6
gnu: r-variantannotation: Update to 1.28.11.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
2019-03-08 09:14:00 +01:00
fff11bccc6
gnu: r-genomeinfodb: Update to 1.18.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
2019-03-08 09:14:00 +01:00
8972989e10
gnu: r-dexseq: Update to 1.28.2.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
2019-03-08 09:14:00 +01:00
3b296475bf
gnu: cd-hit: Support longer sequences.
...
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make
flags.
2019-03-07 13:38:01 +01:00
8035819f4c
gnu: r-org-mm-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): ...to here.
2019-03-06 21:43:33 +01:00
d56df35a25
gnu: r-org-hs-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): ...to here.
2019-03-06 21:42:39 +01:00
f8780e96ff
gnu: r-org-dm-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-dm-eg-db): ...to here.
2019-03-06 21:41:48 +01:00
3a08940e1a
gnu: r-org-ce-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-ce-eg-db): ...to here.
2019-03-06 21:35:20 +01:00
7bc5d1b0e1
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Move from here...
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
...to here.
2019-03-06 21:33:17 +01:00
13dabd6947
gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
...to here.
2019-03-06 21:31:41 +01:00
0c792ffbd1
gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here.
2019-03-06 21:30:30 +01:00
b7d93cf508
gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here.
2019-03-06 21:29:20 +01:00
c3adc83054
gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here.
2019-03-06 21:26:54 +01:00
5acb9052cf
gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here.
2019-03-06 21:25:18 +01:00
fe0b76e215
gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
2019-03-06 21:23:42 +01:00
40a6505711
gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
...to here.
2019-03-06 21:23:20 +01:00
66e35ce63b
gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move
from here...
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to
here.
2019-03-06 21:16:33 +01:00
bfb93b4889
gnu: r-geneplotter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here...
* gnu/packages/bioconductor.scm (r-geneplotter): ...to here.
2019-03-06 21:13:38 +01:00
3d13b448e5
gnu: r-copynumber: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copynumber): Move from here...
* gnu/packages/bioconductor.scm (r-copynumber): ...to here.
2019-03-06 21:07:49 +01:00
38502a7d13
gnu: bismark: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (bismark): Update to 0.20.1.
[source]: Remove obsolete snippet.
[arguments]: Add build phase "replace-plotly.js" and add requried modules;
adjust "install" phase.
[inputs]: Add perl-carp and perl-getopt-long.
[native-inputs]: Add plotly.js and uglify-js.
2019-03-06 16:26:23 +01:00
cb66fb101f
gnu: Add r-scde.
...
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06 15:55:54 +01:00
afeb10a056
gnu: Add bowtie1.
...
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06 15:32:45 +01:00
4fc9b5b1dd
gnu: Add genrich.
...
* gnu/packages/bioinformatics.scm (genrich): New variable.
2019-03-06 13:28:45 +01:00
1fe9a36173
gnu: r-dnacopy: Remove duplicate definition.
...
Reported by Christopher Baines <mail@cbaines.net>.
* gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable.
2019-03-06 10:39:28 +01:00
c335df433f
gnu: pigx-chipseq: Update to 0.0.31.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.31.
2019-03-02 22:05:30 +01:00
a27ca96f10
gnu: Add velvet.
...
* gnu/packages/bioinformatics.scm (velvet): New variable.
2019-03-01 12:55:35 +01:00
0ce256dc79
gnu: discrover: Remove indirect TexLive dependencies.
...
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove
texlive-generic-ifxetex, texlive-latex-oberdiek, texlive-latex-url, and
texlive-latex-xcolor from texlive-union.
2019-03-01 12:55:35 +01:00
8aa1ca85ac
gnu: flexbar: Fix reproducibility bug.
...
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Add phase
"do-not-tune-to-CPU".
2019-02-27 15:40:46 +01:00
cc842b58af
gnu: pigx-chipseq: Update to 0.0.21.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.21.
2019-02-25 15:40:12 +01:00
3ca1d917b6
gnu: discrover: Replace "texlive" with a texlive-union.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"fix-latex-errors"; add build phase "setenv-HOME".
[inputs]: Add rmath-standalone.
[native-inputs]: Replace "texlive" with a texlive-union consisting of
texlive-fonts-cm, texlive-fonts-amsfonts, texlive-generic-ifxetex,
texlive-latex-doi, texlive-latex-examplep, texlive-latex-hyperref,
texlive-latex-ms, texlive-latex-natbib, texlive-bibtex,
texlive-latex-oberdiek, texlive-latex-pgf, texlive-latex-url,
texlive-latex-verbatimbox, and texlive-latex-xcolor.
2019-02-25 15:05:35 +01:00
2e125ece09
gnu: pplacer: Remove the package, which is affected by a CVE on ocaml@4.01.
...
This makes progress towards fixing <https://bugs.gnu.org/27462 >.
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove
variables.
2019-02-19 22:37:02 +01:00
61506fe551
gnu: Remove unneeded uses of python{,2}-minimal.
...
The "python-minimal" package exists mostly to resolve a dependency cycle. To
reduce duplication, packages should prefer the regular Python variants.
* gnu/packages/admin.scm (htop)[native-inputs]: Change PYTHON-MINIMAL-WRAPPER
to PYTHON-WRAPPER.
* gnu/packages/crypto.scm (botan)[native-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Change
PYTHON-MINIMAL to PYTHON.
* gnu/packages/dictionaries.scm (apertium)[native-inputs]: Likewise.
* gnu/packages/databases.scm (mongodb)[native-inputs]: Change PYTHON2-MINIMAL
to PYTHON2.
* gnu/packages/games.scm (openttd-opensfx, openttd-openmsx)[native-inputs]:
Likewise.
* gnu/packages/gnome.scm (deja-dup)[native-inputs]: Likewise.
2019-02-17 18:44:18 +01:00
9846ec0bea
gnu: Add python-pyfit-sne.
...
* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable.
2019-02-15 11:03:26 +01:00
155194d97d
gnu: python-pybedtools: Update to 0.8.0 and fix build.
...
From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 10 Feb 2019 23:39:25 -0500
Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build.
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0.
[phases]{disable-broken-tests}: Do not disable "test_issue_157" and
"test_to_dataframe" tests. Disable the "test_getting_example_beds".
{remove-cython-generated-files}: Add phase.
{generate-cython-extensions}: Add phase.
{check}: Move from python2-pybedtools to here. Add a scripts
subdirectory of the build directory to the PATH, so that the tests can call
them. Invoke pytest rather than nosetests.
[modules]: Move from python2-pybedtools to here.
[propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.26.
[native-inputs]: Replace python-nose by python-pytest and add python-psutil.
2019-02-12 17:16:05 +01:00
385d7546e1
gnu: Add cnvkit.
...
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12 15:41:02 +01:00
307182d4f7
gnu: rcas-web: Update to 0.1.0.
...
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.1.0.
[inputs]: Replace guile2.2-redis with guile-redis.
2019-02-08 22:45:12 +01:00
6df215f8c8
gnu: star: Update to 2.7.0b.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0b.
[arguments]: Add "add-missing-header" build phase.
2019-02-06 21:32:16 +01:00
ba123b6dda
gnu: star: Update to 2.7.0a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0a.
2019-01-30 15:44:47 +01:00
1d1e3676ba
gnu: r-genomicfeatures: Update to 1.34.2.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.2.
2019-01-28 16:27:35 +01:00
ea0eaf537a
gnu: r-variantannotation: Update to 1.28.10.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.10.
2019-01-28 16:27:35 +01:00
5d9b140b29
gnu: r-qtl: Update to 1.44-9.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.44-9.
2019-01-28 16:27:34 +01:00
439d821a3b
gnu: r-optparse: Update to 1.6.1.
...
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.1.
2019-01-28 16:27:33 +01:00
0791437f97
gnu: Move most packages from guile.scm to new module.
...
* gnu/packages/guile.scm (artanis, guildhall, guile-aspell, guile-bash,
guile-8sync, guile-daemon, guile-dsv, guile-fibers, guile-syntax-highlight,
guile-sjson, guile-colorized, guile-pfds, guile-aa-tree, guile-simple-zmq,
jupyter-guile-kernel, guile-sparql, guile-debbugs, guile-email,
guile-debbugs-next, guile-newt, guile-mastodon, guile-parted, guile-xosd,
guile-dbi, guile-dbd-sqlite3, guile-config, guile-hall, guile-ics, guile-wisp,
guile-sly, g-wrap, guile-miniadapton, guile-reader, guile2.2-reader,
guile-ncurses, guile-ncurses/gpm, guile-lib, guile2.0-lib, guile2.2-lib,
guile-minikanren, guile2.0-minikanren, guile2.2-minikanren, guile-irregex,
guile2.0-irregex, guile2.2-irregex, haunt, guile2.0-haunt, guile2.2-haunt,
guile-redis, guile2.0-redis, guile2.2-redis, guile-commonmark,
guile2.0-commonmark, guile2.2-commonmark, mcron, mcron2): Move these variables
from here...
* gnu/packages/guile-xyz.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/installer.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/ci.scm,
gnu/packages/gtk.scm,
gnu/packages/guile.scm,
gnu/packages/mail.scm,
gnu/packages/package-management.scm,
gnu/packages/skribilo.scm,
gnu/packages/web.scm,
gnu/services/mcron.scm: Update module references.
2019-01-28 14:57:10 +01:00
fdb0b40b0e
gnu: pepr: Use PYPI-URI.
...
* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
2019-01-25 23:27:25 +01:00
4cd7c58cf1
gnu: python2-warpedlmm: Use PYPI-URI.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.
2019-01-25 23:26:50 +01:00
4fec042b54
gnu: Move Python compression packages to new module.
...
* gnu/packages/compression.scm (python-lzo, python2-lzo, python-lz4,
python2-lz4, python-lzstring, python2-lzstring, bitshuffle,
bitshuffle-for-snappy): Move variables from here...
* gnu/packages/python-compression.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/bioinformatics.scm,
gnu/packages/java-compression.scm,
gnu/packages/xorg.scm: Adjust module references.
2019-01-15 17:45:33 +01:00
44d10b1f72
gnu: Separate Python core packages from the rest.
...
* gnu/packages/python.scm: Move hundreds of package definitions from here...
* gnu/packages/python-xyz.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/audio.scm,
gnu/packages/backup.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/calendar.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/cluster.scm,
gnu/packages/compression.scm,
gnu/packages/connman.scm,
gnu/packages/crypto.scm,
gnu/packages/cups.scm,
gnu/packages/databases.scm,
gnu/packages/dav.scm,
gnu/packages/direct-connect.scm,
gnu/packages/disk.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/docker.scm,
gnu/packages/ebook.scm,
gnu/packages/elf.scm,
gnu/packages/emacs.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm,
gnu/packages/finance.scm,
gnu/packages/fltk.scm,
gnu/packages/fontutils.scm,
gnu/packages/freedesktop.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/geo.scm,
gnu/packages/gl.scm,
gnu/packages/glib.scm,
gnu/packages/gnome.scm,
gnu/packages/gnupg.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/gtk.scm,
gnu/packages/ham-radio.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/kde-frameworks.scm,
gnu/packages/key-mon.scm,
gnu/packages/libffi.scm,
gnu/packages/libreoffice.scm,
gnu/packages/libusb.scm,
gnu/packages/lirc.scm,
gnu/packages/logging.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/mate.scm,
gnu/packages/maths.scm,
gnu/packages/medical.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mp3.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/nutrition.scm,
gnu/packages/openldap.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/photo.scm,
gnu/packages/polkit.scm,
gnu/packages/protobuf.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/qt.scm,
gnu/packages/rdf.scm,
gnu/packages/ruby.scm,
gnu/packages/search.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/simulation.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/sync.scm,
gnu/packages/terminals.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/virtualization.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wicd.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xorg.scm: Update module references.
2019-01-15 14:46:44 +01:00
14bba460ab
gnu: r-biocgenerics: Move to bioconductor.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
2019-01-13 13:04:18 +01:00
7097c7009d
gnu: r-annotate: Move to bioconductor.
...
* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.
2019-01-13 13:04:18 +01:00
c80fb90f4a
gnu: r-vegan: Move from bioinformatics to cran.
...
* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.
2019-01-13 13:04:18 +01:00
c476edc2cd
gnu: r-rtracklayer: Update to 1.42.1.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
2019-01-12 23:35:18 +01:00
1e107b0960
gnu: r-scater: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
0f268bb275
gnu: r-singlecellexperiment: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
2019-01-12 23:35:18 +01:00
a0224bd4f6
gnu: r-rhdf5lib: Update to 1.4.2.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
2019-01-12 23:35:18 +01:00
40561d0249
gnu: r-hdf5array: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
ad10b3979d
gnu: r-qvalue: Update to 2.14.1.
...
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
2019-01-12 23:35:18 +01:00
19cacb5a2d
gnu: r-gviz: Update to 1.26.4.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
2019-01-12 23:35:18 +01:00
c80595935d
gnu: r-biovizbase: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
2019-01-12 23:35:18 +01:00
27194effd7
gnu: r-ensembldb: Update to 2.6.3.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
2019-01-12 23:35:18 +01:00
43931ff72f
gnu: r-dirichletmultinomial: Update to 1.24.1.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
2019-01-12 23:35:18 +01:00
15d89fe9f8
gnu: r-gage: Update to 2.32.1.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
2019-01-12 23:35:18 +01:00
4615cf9f1a
gnu: r-annotationhub: Update to 2.14.2.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
2019-01-12 23:35:18 +01:00
ab4a862ab8
gnu: r-edaseq: Update to 2.16.3.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.
2019-01-12 23:35:18 +01:00
3bdc41b352
gnu: r-deseq: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
2019-01-12 23:35:18 +01:00
9abf344f8b
gnu: r-msnid: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
2019-01-12 23:35:17 +01:00
880ed11e9f
gnu: r-msnbase: Update to 2.8.3.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
2019-01-12 23:35:17 +01:00
6451af78e1
gnu: r-mzid: Update to 1.20.1.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
2019-01-12 23:35:17 +01:00
a4f038dc97
gnu: r-mzr: Update to 2.16.1.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
2019-01-12 23:35:17 +01:00
46508c3a92
gnu: r-sva: Update to 3.30.1.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
2019-01-12 23:35:17 +01:00
c20426ec5c
gnu: r-methylkit: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
2019-01-12 23:35:17 +01:00
5c72ebafeb
gnu: r-copywriter: Update to 2.14.1.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
2019-01-12 23:35:17 +01:00
86162c767e
gnu: r-rhdf5: Update to 2.26.2.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
2019-01-12 23:35:17 +01:00
4c7b9222dd
gnu: r-tximport: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
2019-01-12 23:35:17 +01:00
4bfde52178
gnu: r-genomicalignments: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
2019-01-12 23:35:17 +01:00
1fa12b2f06
gnu: r-biostrings: Update to 2.50.2.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
2019-01-12 23:35:17 +01:00
d4fc834cf7
gnu: r-biocparallel: Update to 1.16.5.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
2019-01-12 23:35:17 +01:00
52c977a05b
gnu: r-limma: Update to 3.38.3.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
2019-01-12 23:35:17 +01:00
3fd48846eb
gnu: r-variantannotation: Update to 1.28.8.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
2019-01-12 23:35:17 +01:00
a619850930
gnu: r-edger: Update to 3.24.3.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
2019-01-12 23:35:17 +01:00
00f105fe20
gnu: r-biocviews: Update to 1.50.10.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
2019-01-12 23:35:16 +01:00
9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
2019-01-12 23:35:16 +01:00
3b8c884285
gnu: r-rbgl: Update to 1.58.1.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
2019-01-12 23:35:16 +01:00
ffe16ef33c
gnu: r-dexseq: Update to 1.28.1.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
2019-01-12 23:35:16 +01:00
f7e95c50b8
gnu: r-deseq2: Update to 1.22.2.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
2019-01-12 23:35:16 +01:00
feb561f721
gnu: r-scran: Update to 1.10.2.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
2019-01-12 23:35:16 +01:00
80c4e75b87
gnu: r-seqminer: Update to 7.1.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
2019-01-12 23:35:16 +01:00
3bc0667f3c
gnu: r-bookdown: Update to 0.9.
...
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
2019-01-12 23:35:16 +01:00
24155bf40d
gnu: Move Java compression packages to new module.
...
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.
2019-01-12 12:14:28 +01:00
e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
...
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
6fd2ed23ac
gnu: mantis: Limit to x86_64-linux.
...
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
e942813aac
gnu: Add mantis.
...
* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07 11:56:18 +01:00
8894668cd2
gnu: discrover: Comment on attempt of minimal texlive-union.
...
* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
texlive-union.
2018-12-20 12:07:40 +01:00
2f3977b9a7
gnu: gess: Don't hardcode python version.
...
* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
2018-12-17 12:08:05 +02:00
9718265eec
gnu: mash: Use C++ 14.
...
I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,
tweak the compilation to allow it to build with 0.7. The package also builds
with the current version of capnproto. I got the idea of changing the c++
version from here [1].
1: https://github.com/marbl/Mash/issues/98
* gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
2018-12-05 20:29:12 +00:00
42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
2018-12-04 16:21:50 +01:00
4b2d1dc4dc
gnu: bless: Adjust to zlib static output.
...
* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
2018-11-24 19:32:48 +01:00
f028823c0f
gnu: mosaik: Fix FTBFS from b90289dadc.
...
* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-24 15:57:56 +01:00
d57ec906ba
gnu: pigx-scrnaseq: Use latest snakemake.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:48 +01:00
92d9a1e2c6
gnu: pigx-bsseq: Use latest snakemake.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:16 +01:00
c068d00746
gnu: pigx-chipseq: Use latest snakemake.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:29:35 +01:00
93d229cb86
gnu: python-loompy: Remove python-typing.
...
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
2018-11-23 15:59:44 +01:00
4f70db97a0
Merge branch 'master' into core-updates
2018-11-20 01:14:12 +01:00
c2e26dc156
gnu: r-ensembldb: Update to 2.6.2.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
2018-11-19 16:46:32 +01:00
e038819138
gnu: r-msnbase: Update to 2.8.1.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
2018-11-19 16:46:00 +01:00
4535a7b0f5
gnu: r-genomeinfodb: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
2018-11-19 16:33:35 +01:00
30f0d21b40
gnu: Add nanopolish.
...
* gnu/packages/bioinformatics.scm (nanopolish): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15 22:23:57 +01:00
2d86eaff5b
gnu: sambamba: Update to 0.6.8.
...
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-15 13:09:01 +01:00
2e0f69057a
gnu: bioinformatics: Return #t from all phases and snippets.
...
* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
2018-11-14 23:44:18 -05:00
ee66a13563
gnu: Add jamm.
...
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
...
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13 23:34:40 +01:00
314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
13e70f6304
gnu: r-go-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13 23:34:39 +01:00
5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-11 23:13:48 +01:00
03a415365a
gnu: r-ensembldb: Update to 2.6.1.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
2018-11-09 19:41:54 +01:00
88514b9124
gnu: r-biostrings: Update to 2.50.1.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
2018-11-09 19:41:53 +01:00
77bea84ba1
gnu: r-biocviews: Update to 1.50.5.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
2018-11-09 19:41:53 +01:00
a1e83a9856
gnu: pplacer-scripts: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 10:06:35 +01:00
ce49fdcce9
gnu: roary: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 09:58:05 +01:00
a9542937c8
gnu: seek: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
2018-11-08 09:54:22 +01:00
9f527c9199
gnu: sailfish: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
2018-11-08 09:52:46 +01:00
86c6928ea3
gnu: vsearch: Update to 2.9.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
2018-11-08 09:46:42 +01:00
15c9609482
gnu: sra-tools: Update to 2.9.3.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
2018-11-08 09:46:05 +01:00
b17333414f
gnu: plink-ng: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
2018-11-08 09:30:59 +01:00
87408854ec
gnu: ncbi-vdb: Update to 2.9.3.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
2018-11-08 09:30:16 +01:00
8d3eaa9262
gnu: ngs-sdk: Update to 2.9.3.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
2018-11-08 09:29:58 +01:00
3da3cedf76
gnu: ngs-sdk: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:15:05 +01:00
e78e54d029
gnu: emboss: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:14:09 +01:00
8b685c4720
gnu: taxtastic: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:13:35 +01:00
2e2d88539c
gnu: sra-tools: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:12:43 +01:00
179416467f
gnu: muscle: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:11:38 +01:00
0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
e35dce0170
gnu: mash: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
...
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
c527d36f02
gnu: java-picard-1.113: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
2018-11-08 09:02:34 +01:00
e438c96558
gnu: fraggenescan: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
2018-11-08 08:58:46 +01:00
c098c49b3e
gnu: sailfish: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
4031e7f1ec
gnu: ngs-sdk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
2018-11-08 08:53:53 +01:00
6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
2018-11-08 08:53:53 +01:00
3398dfb764
gnu: ncbi-vdb: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
2018-11-08 08:53:53 +01:00
e0f1aa2d2b
gnu: tadbit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
2018-11-08 08:53:50 +01:00
f3f34b132c
gnu: filevercmp: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
2018-11-07 23:17:36 +01:00
3b888065da
gnu: ritornello: Update to 2.0.1.
...
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
2018-11-07 23:17:36 +01:00
7145f4e519
gnu: ritornello: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
e0a8fc85dd
gnu: snap-aligner: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
2018-11-07 23:17:35 +01:00
6236524409
gnu: sortmerna: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
273df99d7d
gnu: vsearch: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
67caa4b773
gnu: preseq: Update to 2.0.3.
...
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
2018-11-07 23:17:35 +01:00
37e285be43
gnu: preseq: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
63f3255e13
gnu: seqtk: Update to 1.3.
...
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
2018-11-07 23:17:35 +01:00
019fcdf20a
gnu: seqtk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
b9d0c3564b
gnu: raxml: Update to 8.2.12.
...
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
2018-11-07 23:17:34 +01:00
d9ba126d17
gnu: python2-biom-format: Fix build.
...
This is a follow-up to commit 239716fb0b
2018-11-07 23:17:34 +01:00
4715d4af17
gnu: raxml: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
5e242b02c3
gnu: pyicoteo: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
2b773a9273
gnu: sra-tools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
55698df260
gnu: libgff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
4257c10ad2
gnu: kentutils: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
2018-11-07 21:41:55 +01:00
1a20bcadf3
gnu: r-seqgl: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
a2b9d6a8d0
gnu: pplacer: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
2018-11-07 21:41:55 +01:00
6052264b56
gnu: minced: Update to 0.3.2.
...
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07 21:41:55 +01:00
9d94ca0ebf
gnu: minced: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
b58d9e4aa2
gnu: metabat: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
5c1f35e71b
gnu: mash: Update to 2.1.
...
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
497fc04d8f
gnu: mash: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
2dc28391f3
gnu: kaiju: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
6fe323bf2e
gnu: kaiju: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
2018-11-07 20:46:36 +01:00
f0731591a5
gnu: idr: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
b8a6230df3
gnu: java-htsjdk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07 20:36:07 +01:00
57be690d91
gnu: hisat2: Use versioned source URL.
...
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
c8f02c1dcb
gnu: grit: Update to 2.0.5.
...
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
8d75adbf03
gnu: grit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
152bebd9e0
gnu: gemma: Update to 0.98.
...
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
2018-11-07 20:26:46 +01:00
b113f39019
gnu: gemma: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
91b71cfbba
gnu: fxtract: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
239716fb0b
gnu: python-biom-format: Update to 2.1.7.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07 19:47:07 +01:00
007a81d5cf
gnu: python-biom-format: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
2018-11-07 19:10:36 +01:00
383cb7b8e6
gnu: bioawk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
2018-11-07 18:52:46 +01:00
8e58319c45
gnu: bamtools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
21335fdbec
gnu: ngless: Install links to required tools.
...
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07 17:19:53 +01:00
fff67cc8a7
gnu: prodigal: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
9255198423
gnu: r-mzr: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
2018-11-07 12:27:16 +01:00
37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
2018-11-07 12:27:16 +01:00
8e48d36f26
gnu: r-hdf5array: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
2018-11-07 12:27:16 +01:00
611a255d2b
gnu: r-rhdf5: Update to 2.26.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
2018-11-07 12:27:16 +01:00
a1c2bf8e54
gnu: r-rcas: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
2018-11-07 12:27:16 +01:00
900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
2018-11-07 12:27:16 +01:00
70a3a76ba7
gnu: r-scran: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus