4adb40bffc
Merge branch 'master' into core-updates
2018-01-11 14:22:50 -08:00
f6e2d86f8e
gnu: seqmagick: Use 'pypi-uri'.
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* gnu/packages/bioinformatics.scm (seqmagick)[source]: Use 'pypi-uri'.
2018-01-10 20:16:36 +10:00
3146f22dec
gnu: mafft: Update to 7.313.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.313.
[source]: Use HTTPS URI.
2018-01-10 20:16:36 +10:00
39fb853abe
gnu: seqmagick: Update to 0.7.0.
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* 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
4ed41f472b
Merge branch 'master' into core-updates
2018-01-03 14:18:01 -05:00
8057dee15b
gnu: htslib: Mark up description.
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* gnu/packages/bioinformatics.scm (htslib)[description]: Use @command{}.
2018-01-02 16:13:23 +01:00
7edee34427
gnu: ribotaper: Wrap executables.
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* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Add phase
"wrap-executables".
2018-01-02 12:07:06 +01:00
6856518456
gnu: python-pysam: Update to 0.13.0.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.13.0.
2018-01-02 02:13:38 +01:00
ddf38ece8a
gnu: htslib: Update to 1.6.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.6.
2018-01-02 01:47:42 +01:00
23de2e1d5f
Merge remote-tracking branch 'origin/master' into core-updates
2017-12-31 14:10:25 +02:00
f14a6586ec
gnu: vsearch: Update to 2.6.2.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.2.
2017-12-27 22:12:08 +10:00
e9960d8cba
gnu, doc: Use HTTPS for cran.r-project.org home pages.
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* 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
b9bf2b8985
gnu: Update r-mutationalpatterns to 1.4.2.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.2.
2017-12-22 12:23:06 +01:00
f76fc96866
Merge branch 'master' into core-updates
2017-12-21 13:58:35 -05:00
b9e8a5c594
gnu: r-biomart: Update to 2.34.1.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1.
[propagated-inputs]: Add r-httr.
2017-12-19 20:35:04 +01:00
11e42209a8
gnu: r-gviz: Update to 1.22.2.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
2017-12-19 20:35:04 +01:00
2ccd850192
gnu: r-gqtlstats: Update to 1.10.1.
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* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
2017-12-19 20:35:04 +01:00
28d25d037e
gnu: r-rtracklayer: Update to 1.38.2.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
2017-12-19 20:35:04 +01:00
d41f678420
gnu: r-limma: Update to 3.34.4.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
2017-12-19 20:35:03 +01:00
ab0dd8ac10
gnu: r-edger: Update to 3.20.2.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
2017-12-19 20:35:03 +01:00
7665fb39f5
gnu: r-biocstyle: Update to 2.6.1.
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* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
2017-12-19 20:35:03 +01:00
756ac7254c
gnu: r-dexseq: Update to 1.24.2.
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* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
2017-12-19 20:35:03 +01:00
8d11ef4470
gnu: r-vegan: Update to 2.4-5.
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* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
2017-12-19 20:35:02 +01:00
677bc34d5b
gnu: Remove redundant cmake libdir configure flags.
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* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove
CMAKE_INSTALL_LIBDIR flag.
* gnu/packages/calendar.scm (libical): Same.
* gnu/packages/engineering.scm (kicad): Same.
* gnu/packages/games.scm (openrct2, mgba): Same.
* gnu/packages/gl.scm (virtualgl): Same.
* gnu/packages/image-processing.scm (mia): Same.
* gnu/packages/linux.scm (rdma-core): Same.
* gnu/packages/machine-learning.scm (dlib): Same.
* gnu/packages/maths.scm (lapack, superlu, z3): Same.
* gnu/packages/password-utils.scm (keepassxc): Same.
* gnu/packages/photo.scm (darktable): Same.
* gnu/packages/rdesktop.scm (freerdp): Same.
2017-12-19 19:52:01 +02:00
f1a2b1cb20
gnu: r-seurat: Update to 2.1.0.
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* 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
8271b8d22a
gnu: r-seurat: Fix ModularityOptimizer.jar.
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* gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class
attribute in manifest.
2017-12-18 12:01:34 +01:00
6098a386a9
gnu: bedtools: Update to 2.27.1.
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* gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
2017-12-15 13:56:51 +10:00
4e0b3583ea
gnu: diamond: Update to 0.9.14.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
2017-12-14 22:50:10 +10:00
9cf5f134d5
gnu: Switch to using the version-major procedure.
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* 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
83b9d121a7
gnu: bedtools-2.18: Fix build.
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* 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
0d9824cc12
gnu: bedtools: Update to 2.27.0.
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* 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
d112e5a8c2
gnu: Add kallisto.
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* gnu/packages/bioinformatics.scm (kallisto): New variable.
2017-12-03 18:38:58 +01:00
117d8cc40e
gnu: jellyfish: Update to 2.2.7.
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* 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
9b8d02011f
gnu: r-annotationhub: Update to 2.10.1.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
2017-11-30 17:28:24 +01:00
87e91a9fff
gnu: r-msnid: Update to 1.12.1.
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* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
2017-11-30 17:28:23 +01:00
439492654b
gnu: r-maldiquant: Update to 1.17.
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* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
2017-11-30 17:28:23 +01:00
06e8e0fc6c
gnu: r-genomicalignments: Update to 1.14.1.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
2017-11-30 17:28:22 +01:00
1ce5d32b49
gnu: r-limma: Update to 3.34.2.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
2017-11-30 17:28:22 +01:00
8131cf4162
gnu: r-variantannotation: Update to 1.24.2.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
2017-11-30 17:28:21 +01:00
d2081a17ed
gnu: r-getopt: Update to 1.20.1.
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* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
2017-11-30 17:28:20 +01:00
4220ab0c81
gnu: r-gseabase: Update to 1.40.1.
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* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
2017-11-30 17:28:20 +01:00
d259932ca8
gnu: r-dexseq: Update to 1.24.1.
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* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
2017-11-30 17:28:19 +01:00
058644c0f2
gnu: r-deseq2: Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
2017-11-30 17:28:18 +01:00
654c29aceb
gnu: r-annotate: Update to 1.56.1.
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* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
2017-11-30 17:28:18 +01:00
9364a520ce
gnu: metabat: Use scons-build-system.
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* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
2017-11-30 18:19:32 +05:30
1fd904fb38
gnu: Update r-mutationalpatterns to 1.4.1.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
2017-11-29 14:56:28 +01:00
efa6a1ddb5
gnu: Add r-copynumber.
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* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
2017-11-29 12:46:17 +01:00
d7f24778de
gnu: Add java-picard-1.113.
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* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
2017-11-27 12:12:41 +01:00
d7fed31ad2
gnu: Add java-picard.
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* gnu/packages/bioinformatics.scm (java-picard): New variable.
2017-11-27 12:12:40 +01:00
bd94b6f850
gnu: java-htsjdk: Update to 2.3.0.
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* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0.
[arguments]: Build with JDK 8.
[inputs]: Add java-ngs, java-snappy, java-commons-compress,
java-commons-logging-minimal, java-commons-jexl-2, and java-xz.
[native-inputs]: Add java-testng.
2017-11-27 12:12:40 +01:00
Leo Famulari