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Author SHA1 Message Date
Ricardo Wurmus
625cdc3fde
gnu: star: Make reproducible. 
* gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase
"make-reproducible".
 2018-01-22 22:49:10 +01:00
Efraim Flashner
3df57b3a97
gnu: khmer: Add aarch64-linux to supported systems. 
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: Add
aarch64-linux to the supported systems.
 2018-01-22 09:39:59 +02:00
Ricardo Wurmus
7762646d95
gnu: Add salmon. 
* gnu/packages/bioinformatics.scm (libstadenio-for-salmon,
spdlog-for-salmon, bwa-for-salmon, salmon): New variables.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus
8d77a085a7
gnu: Add sailfish. 
* gnu/packages/bioinformatics.scm (sailfish): New variable.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus
1fe0bde34d
gnu: Add libdivsufsort. 
* gnu/packages/bioinformatics.scm (libdivsufsort): New variable.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus
c3b2ab9d3b
gnu: Add libgff. 
* gnu/packages/bioinformatics.scm (libgff): New variable.
 2018-01-21 14:18:09 +01:00
Ben Woodcroft
f6e2d86f8e
gnu: seqmagick: Use 'pypi-uri'. 
* gnu/packages/bioinformatics.scm (seqmagick)[source]: Use 'pypi-uri'.
 2018-01-10 20:16:36 +10:00
Ben Woodcroft
3146f22dec
gnu: mafft: Update to 7.313. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.313.
[source]: Use HTTPS URI.
 2018-01-10 20:16:36 +10:00
Ben Woodcroft
39fb853abe
gnu: seqmagick: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0.  Use
python-3.
[arguments]: Remove replacement phase for check.
[inputs]: Add biopython.  Remove python2-biopython-1.66.
(python2-biopython-1.66): Remove variable.
 2018-01-09 22:39:05 +10:00
Tobias Geerinckx-Rice
8057dee15b
gnu: htslib: Mark up description. 
* gnu/packages/bioinformatics.scm (htslib)[description]: Use @command{}.
 2018-01-02 16:13:23 +01:00
Ricardo Wurmus
7edee34427
gnu: ribotaper: Wrap executables. 
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Add phase
"wrap-executables".
 2018-01-02 12:07:06 +01:00
Tobias Geerinckx-Rice
6856518456
gnu: python-pysam: Update to 0.13.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.13.0.
 2018-01-02 02:13:38 +01:00
Tobias Geerinckx-Rice
ddf38ece8a
gnu: htslib: Update to 1.6. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.6.
 2018-01-02 01:47:42 +01:00
Ben Woodcroft
f14a6586ec
gnu: vsearch: Update to 2.6.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.2.
 2017-12-27 22:12:08 +10:00
Tobias Geerinckx-Rice
e9960d8cba
gnu, doc: Use HTTPS for cran.r-project.org home pages. 
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
 2017-12-24 16:12:13 +01:00
Roel Janssen
b9bf2b8985
gnu: Update r-mutationalpatterns to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.2.
 2017-12-22 12:23:06 +01:00
Ricardo Wurmus
b9e8a5c594
gnu: r-biomart: Update to 2.34.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1.
[propagated-inputs]: Add r-httr.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
11e42209a8
gnu: r-gviz: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
2ccd850192
gnu: r-gqtlstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
28d25d037e
gnu: r-rtracklayer: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
d41f678420
gnu: r-limma: Update to 3.34.4. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
ab0dd8ac10
gnu: r-edger: Update to 3.20.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
7665fb39f5
gnu: r-biocstyle: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
756ac7254c
gnu: r-dexseq: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
8d11ef4470
gnu: r-vegan: Update to 2.4-5. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
 2017-12-19 20:35:02 +01:00
Ricardo Wurmus
f1a2b1cb20
gnu: r-seurat: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0.
[propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica,
r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr,
r-rcppeigen, r-fastica.
 2017-12-18 12:01:35 +01:00
Ricardo Wurmus
8271b8d22a
gnu: r-seurat: Fix ModularityOptimizer.jar. 
* gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class
attribute in manifest.
 2017-12-18 12:01:34 +01:00
Ben Woodcroft
6098a386a9
gnu: bedtools: Update to 2.27.1. 
* gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
 2017-12-15 13:56:51 +10:00
Ben Woodcroft
4e0b3583ea
gnu: diamond: Update to 0.9.14. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
 2017-12-14 22:50:10 +10:00
Christopher Baines
9cf5f134d5
gnu: Switch to using the version-major procedure. 
* gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major.
  (hmmer)[source]: Switch to using version-major.
  (pidgin)[native-search-paths]: Switch to using version-major.
  (r-minimal)[source]: Switch to using version-major.
 2017-12-11 19:12:33 +00:00
Ricardo Wurmus
83b9d121a7
gnu: bedtools-2.18: Fix build. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom
install phase.

Reported by Mark H Weaver <mhw@netris.org>.
 2017-12-09 13:01:15 +01:00
Ricardo Wurmus
0d9824cc12
gnu: bedtools: Update to 2.27.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
[arguments]: Remove custom "install" phase; specify prefix.
 2017-12-06 19:13:35 +01:00
Ricardo Wurmus
d112e5a8c2
gnu: Add kallisto. 
* gnu/packages/bioinformatics.scm (kallisto): New variable.
 2017-12-03 18:38:58 +01:00
Ricardo Wurmus
117d8cc40e
gnu: jellyfish: Update to 2.2.7. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7.
[native-inputs]: Add pkg-config.
[inputs]: Add htslib.
 2017-11-30 17:38:36 +01:00
Ricardo Wurmus
9b8d02011f
gnu: r-annotationhub: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
 2017-11-30 17:28:24 +01:00
Ricardo Wurmus
87e91a9fff
gnu: r-msnid: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus
439492654b
gnu: r-maldiquant: Update to 1.17. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus
06e8e0fc6c
gnu: r-genomicalignments: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus
1ce5d32b49
gnu: r-limma: Update to 3.34.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus
8131cf4162
gnu: r-variantannotation: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
 2017-11-30 17:28:21 +01:00
Ricardo Wurmus
d2081a17ed
gnu: r-getopt: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus
4220ab0c81
gnu: r-gseabase: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus
d259932ca8
gnu: r-dexseq: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
 2017-11-30 17:28:19 +01:00
Ricardo Wurmus
058644c0f2
gnu: r-deseq2: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
 2017-11-30 17:28:18 +01:00
Ricardo Wurmus
654c29aceb
gnu: r-annotate: Update to 1.56.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
 2017-11-30 17:28:18 +01:00
Arun Isaac
9364a520ce
gnu: metabat: Use scons-build-system. 
* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
 2017-11-30 18:19:32 +05:30
Roel Janssen
1fd904fb38
gnu: Update r-mutationalpatterns to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
 2017-11-29 14:56:28 +01:00
Roel Janssen
efa6a1ddb5
gnu: Add r-copynumber. 
* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
 2017-11-29 12:46:17 +01:00
Ricardo Wurmus
d7f24778de
gnu: Add java-picard-1.113. 
* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
 2017-11-27 12:12:41 +01:00
Ricardo Wurmus
d7fed31ad2
gnu: Add java-picard. 
* gnu/packages/bioinformatics.scm (java-picard): New variable.
 2017-11-27 12:12:40 +01:00