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783 Commits

Author SHA1 Message Date
Roel Janssen b2fff403c8
gnu: r-biobase: Update to 2.36.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.0.
 2017-04-28 11:04:44 +02:00
Roel Janssen 1859712bef
gnu: r-genomicranges: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.0.
 2017-04-28 11:04:42 +02:00
Roel Janssen 17a02f5149
gnu: r-xvector: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.16.0.
 2017-04-28 11:04:42 +02:00
Roel Janssen abf5a14e11
gnu: r-limma: Update to 3.32.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.0.
 2017-04-28 11:04:41 +02:00
Roel Janssen d2d7af9832
gnu: r-variantannotation: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.0.
 2017-04-28 11:04:40 +02:00
Roel Janssen 00ffd55fa1
gnu: r-edger: Update to 3.18.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.18.0.
 2017-04-28 11:04:39 +02:00
Roel Janssen 38b99ccc57
gnu: r-genomeinfodb: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): [source] Update to 1.12.0,
[propagated-inputs]: Add r-genomeinfodbdata.
 2017-04-28 11:04:37 +02:00
Roel Janssen 7d9ab5d920
gnu: r-iranges: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.0.
 2017-04-28 11:04:36 +02:00
Roel Janssen f1f380185b
gnu: r-s4vectors: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.0.
 2017-04-28 11:04:34 +02:00
Roel Janssen 9b02d49cb0
gnu: r-dnacopy: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.0.
 2017-04-28 11:04:33 +02:00
Roel Janssen 2e11beec48
gnu: r-bioccheck: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.12.0.
 2017-04-28 11:04:32 +02:00
Roel Janssen 3bef24c968
gnu: r-biocstyle: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): [source] Update to 2.4.0.
[propagated-inputs]: Add r-bookdown, r-knitr, r-rmarkdown, r-yaml.
 2017-04-28 11:04:31 +02:00
Roel Janssen 68eac34974
gnu: r-biocviews: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.44.0.
 2017-04-28 11:04:30 +02:00
Roel Janssen 3bef15286a
gnu: r-biocinstaller: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.26.0.
 2017-04-28 11:04:28 +02:00
Roel Janssen 28a5b3f2c6
gnu: r-biocgenerics: Update to 0.22.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.22.0.
 2017-04-28 11:04:26 +02:00
Roel Janssen 795a604526
gnu: r-grohmm: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.10.0.
 2017-04-28 11:04:25 +02:00
Roel Janssen 026dc7e4fc
gnu: r-systempiper: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.10.0.
 2017-04-28 11:04:24 +02:00
Roel Janssen 34c276f761
gnu: r-shortread: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.34.0.
 2017-04-28 11:04:22 +02:00
Roel Janssen 9511773423
gnu: r-gostats: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.42.0.
 2017-04-28 11:04:21 +02:00
Roel Janssen ca0289aee7
gnu: r-category: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.0.
 2017-04-28 11:04:20 +02:00
Roel Janssen c584a07ffd
gnu: r-gseabase: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.38.0.
 2017-04-28 11:04:19 +02:00
Roel Janssen 8ab6f241ea
gnu: r-rbgl: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.52.0.
 2017-04-28 11:04:16 +02:00
Roel Janssen 46972a4427
gnu: r-annotationforge: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.0.
 2017-04-28 11:04:12 +02:00
Roel Janssen 3ae74e451c
gnu: r-deseq2: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.0.
 2017-04-28 11:04:09 +02:00
Roel Janssen b5bc3a3963
gnu: r-genefilter: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.58.0.
 2017-04-28 11:04:06 +02:00
Roel Janssen 97a50e4f34
gnu: r-geneplotter: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.54.0.
 2017-04-28 11:03:59 +02:00
Roel Janssen dbab99b6d2
gnu: r-annotate: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.54.0.
 2017-04-28 11:03:47 +02:00
Roel Janssen ffef27f3d2
gnu: Add r-genomeinfodbdata. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
 2017-04-28 10:17:06 +02:00
Roel Janssen 71e34e6b5b
gnu: Add r-delayedarray. 
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
 2017-04-28 10:15:12 +02:00
Roel Janssen 2abfc5b827
gnu: Add r-bookdown. 
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
 2017-04-28 10:09:31 +02:00
Ricardo Wurmus 31c374e081
gnu: python-pysam: Disable tests. 
* gnu/packages/bioinformatics.scm (python-pysam): Disable tests.
 2017-04-25 14:05:59 +02:00
Ricardo Wurmus b2955e224e
gnu: python-pysam: Fix tests, again. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nosetests
explicitly with a single process.
 2017-04-24 18:46:28 +02:00
Efraim Flashner c136240efc
gnu: diamond: Enable building on all architectures. 
* gnu/packages/bioinformatics.scm (diamond)[supported-systems]: Remove
field.
 2017-04-24 19:30:10 +03:00
Ricardo Wurmus 1a84edeb0b
gnu: r-seqminer: Update to 5.9. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.9.
 2017-04-22 23:30:31 +02:00
Ben Woodcroft a7d12a9e71
gnu: proteinortho: Update to 5.16. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16.
 2017-04-21 23:03:56 +10:00
Ben Woodcroft 37199768e8
gnu: diamond: Update to 0.8.38. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.38.
 2017-04-21 23:03:55 +10:00
Tobias Geerinckx-Rice d1e4ad1b02
gnu: Fix typos in descriptions. 
* gnu/packages/admin.scm (di)[description]: Likewise.
* gnu/packages/bioinformatics.scm (r-annotate)[description]: Likewise.
* gnu/packages/datastructures.scm (sparsehash)[description]: Likewise.
* gnu/packages/dns.scm (knot)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-idle-highlight)[synopsis, description]:
Likewise.
* gnu/packages/gnome.scm (libpeas)[description]: Likewise.
* gnu/packages/gtk.scm (python2-pygtk)[description]: Likewise.
* gnu/packages/kde-frameworks.scm (kactivities)[description]: Fix typo.
* gnu/packages/libevent.scm (perl-anyevent)[description]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[description]: Likewise.
* gnu/packages/mail.scm (mlmmj)[description]: Likewise.
* gnu/packages/maths.scm (vc)[description]: Likewise.
* gnu/packages/music.scm (gx-super-fuzz-lv2)[description]: Likewise.
* gnu/packages/networking.scm (nload)[description]: Likewise.
* gnu/packages/python.scm (python-execnet)[description]: Likewise.
* gnu/packages/terminals.scm (tilda)[description]: Likewise.
* gnu/packages/python.scm (python-execnet, python-tables)
(python2-coverage-test-runner, python2-rope)[description]: Likewise.
 2017-04-17 02:04:08 +02:00
Ben Woodcroft 88eb119f95
gnu: mafft: Update to 7.310. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
 2017-04-14 15:19:37 +10:00
Ben Woodcroft e9e0fab079
gnu: raxml: Update to 8.2.10. 
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.10.
 2017-04-09 21:44:14 +10:00
Ricardo Wurmus 6acdff5875
gnu: r-rsamtools: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.2.
 2017-04-09 13:34:53 +02:00
Ricardo Wurmus dc8ebe43af
gnu: r-biocparallel: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.2.
 2017-04-09 13:34:53 +02:00
Ricardo Wurmus 1d65b5379b
gnu: r-vegan: Update to 2.4-3. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-3.
[arguments]: Remove build phase "revert-test-deletion".
[native-inputs]: Remove "r-vegan-delete-tests-patch".
 2017-04-08 10:25:50 +02:00
Ben Woodcroft 37982693ca
gnu: vsearch: Update to 2.4.3. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
 2017-04-07 21:35:07 +10:00
Ricardo Wurmus e18c731ba0
gnu: r-seqinr: Update to 3.3-6. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
 2017-04-06 14:39:22 +02:00
Ricardo Wurmus 0685fe3c86
gnu: r-rcpparmadillo: Update to 0.7.700.0.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0.
[source]: Do not delete bundled armadillo sources, because upstream no longer
hosts previous versions.
[propagated-inputs]: Remove "armadillo-for-rcpparmadillo".
[arguments]: Remove because we no longer need to link with the armadillo
library.
* gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no
longer need to link with armadillo library.
 2017-04-06 14:39:22 +02:00
Ricardo Wurmus a3656b11d2
gnu: r-annotationforge: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
 2017-04-06 14:39:22 +02:00
Ricardo Wurmus e0d7b31820
gnu: r-shortread: Update to 1.32.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 2cea968e41
gnu: r-s4vectors: Update to 0.12.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 7d05eb2dcc
gnu: r-iranges: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus e89cf15091
gnu: r-variantannotation: Update to 1.20.3. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 3506a62762
gnu: r-limma: Update to 3.30.13. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 4cd4721dbb
gnu: r-genomicranges: Update to 1.26.4. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 69b356efce
gnu: r-annotationdbi: Update to 1.36.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 5cc3b7a548
gnu: r-genomicalignments: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 25d8854723
gnu: r-rtracklayer: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 9ce6cb082e
gnu: r-genomicfeatures: Update to 1.26.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 57ac1d2f03
gnu: r-seqminer: Update to 5.7. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
 2017-04-06 14:39:19 +02:00
Ricardo Wurmus e8bec95e69
gnu: r-maldiquant: Update to 1.16.2. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
 2017-04-06 14:39:19 +02:00
Ricardo Wurmus 4cd07e487e
gnu: r-genomeinfodb: Update to 1.10.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3.
[propagated-inputs]: Add "r-rcurl".
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus acbeb2d56b
gnu: r-xvector: Update to 0.14.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus da250f733a
gnu: r-bioccheck: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1.
[propagated-inputs]: Remove "r-knitr" and "r-devtools".
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus 1108a920bd
gnu: sra-tools: Fix glibc naming conflict. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase
"patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
 2017-04-05 18:06:51 +02:00
Ricardo Wurmus beebe43176
gnu: sra-tools: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
 2017-04-05 18:06:51 +02:00
Ben Woodcroft fc5b12879f
gnu: diamond: Update to 0.8.37. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
 2017-04-05 22:49:01 +10:00
Leo Famulari 7bf837fd43
gnu: Use HTTPS URLs for GitHub home-pages. 
* gnu/packages/bioinformatics.scm, gnu/packages/emacs.scm,
gnu/packages/haskell.scm, gnu/packages/libffi.scm, gnu/packages/lisp.scm,
gnu/packages/ocaml.scm, gnu/packages/openstack.scm, gnu/packages/python.scm,
gnu/packages/ruby.scm, gnu/packages/shells.scm, gnu/packages/statistics.scm,
gnu/packages/xdisorg.scm: Use HTTPS URLs for all packages with a home-page on
GitHub.
 2017-04-02 20:00:51 -04:00
Ben Woodcroft cf1d581464
gnu: khmer: Build with gcc-4. 
* gnu/packages/bioinformatics.scm (khmer)[inputs]: Add gcc-4.9.
 2017-04-02 10:14:17 +10:00
Marius Bakke 84157bb8bf
Merge branch 'master' into core-updates 
Most conflicts are from 6fd52309b8.
 2017-03-30 22:59:53 +02:00
Ricardo Wurmus fa702e1a29
gnu: discrover: Add missing includes. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"add-missing-includes" to include "random" headers.
 2017-03-30 10:35:54 +02:00
Ricardo Wurmus 0d2c0562b8
gnu: stringtie: Remove typedef conflict. 
* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting
typedef in a new build phase "remove-duplicate-typedef".
 2017-03-30 10:35:53 +02:00
Ludovic Courtès e1f02f92e9
Replace (compose not PROC) with simpler idioms. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
 2017-03-28 22:15:44 +02:00
Ricardo Wurmus 939b6b113b
gnu: star: Update to 2.5.3a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
 2017-03-23 11:21:08 +01:00
Ricardo Wurmus 54262c5435
gnu: python-pysam: Run tests in parallel. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
 2017-03-22 12:33:28 +01:00
Ricardo Wurmus 71dbf592c4
gnu: python-pysam: Run tests before installation. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
 2017-03-22 12:33:28 +01:00
Ricardo Wurmus 879b521cd0
gnu: python-pysam: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
 2017-03-22 12:33:24 +01:00
Ludovic Courtès f6396d862f
gnu: Rename "guile-next" to "guile". 
* gnu/packages/guile.scm (guile-next): Rename to...
(guile-2.2): ... this.  Update users.
[name]: Change to "guile".
[synopsis]: Remove.
[properties]: Remove 'upstream-name', 'ftp-server', and
'ftp-directory'.
* gnu/packages/bioinformatics.scm (rcas-web): Update accordingly.
* gnu/packages/tls.scm (gnutls/guile-2.2): Likewise.
* tests/guix-build.sh: Use 'guile@2.2' instead of 'guile-next'.
* doc/guix.texi (Package Transformation Options): Update examples that
referred to "guile-next".
 2017-03-19 18:14:22 +01:00
Ricardo Wurmus 2d7c4ae3ee
gnu: r: Rename to r-minimal. 
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus aeb64f3cb2
gnu: r: Do not build recommended packages. 
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
 2017-03-17 10:14:02 +01:00
Raoul Jean Pierre Bonnal 2441c28414
gnu: Add r-seurat. 
* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-03-16 14:54:58 +01:00
Ricardo Wurmus 79849358f8
gnu: sra-tools: Update to 2.8.2-1. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
 2017-03-16 13:40:36 +01:00
Ricardo Wurmus d5e1716239
gnu: ncbi-vdb: Install configuration files. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
 2017-03-16 13:39:53 +01:00
Ricardo Wurmus 558e23074e
gnu: ncbi-vdb: Override search path for java-ngs. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
 2017-03-16 13:38:39 +01:00
Ricardo Wurmus 701111989e
gnu: ncbi-vdb: Use modify-phases syntax. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
 2017-03-16 10:20:56 +01:00
Ricardo Wurmus 5021f54787
gnu: ncbi-vdb: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
 2017-03-16 10:19:25 +01:00
Ricardo Wurmus 6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
 2017-03-16 10:18:48 +01:00
Tobias Geerinckx-Rice f38607536e
gnu: Use INSTALL-FILE where appropriate. 
* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler
INSTALL-FILE for COPY-FILE when invoked with redundant arguments.
* gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity,
edirect, fasttree, rsem, samtools-0.1): Likewise.
* gnu/packages/code.scm (withershins): Likewise.
* gnu/packages/conky.scm (conky): Likewise.
* gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise.
* gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise.
* gnu/packages/engineering.scm (librecad): Likewise.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice b2d748edff
gnu: samtools: End installation phases with truth. 
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]:
Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
 2017-03-15 01:10:30 +01:00
Ben Woodcroft fbf45d6ea7
gnu: vsearch: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
 2017-03-11 11:37:15 +10:00
Raoul Jean Pierre Bonnal 036cd0cb8b
gnu: Add r-ape. 
* gnu/packages/bioinformatics.scm (r-ape): New variable.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Ben J. Woodcroft 79f09fa239
gnu: hmmer: Build reproducibly. 
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.
 2017-03-10 20:31:30 +10:00
Ricardo Wurmus 5ded35d89d
gnu: Add sambamba. 
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
 2017-03-10 10:13:59 +01:00
Marius Bakke 3f98071ac5
Merge branch 'python-tests' 2017-03-03 16:55:43 +01:00
Ben Woodcroft a9f754d733
gnu: diamond: Update to 0.8.36. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
 2017-03-02 21:19:26 +10:00
Ricardo Wurmus 48d66a9c99
gnu: bamtools: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
 2017-02-28 12:10:02 +01:00
Marius Bakke 2bb12f5a68
gnu: ribodiff: Fix test failure. 
* gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK
  and PYTHON2-NOSE.
 2017-02-27 15:32:17 +01:00
Ricardo Wurmus 1885bb0c08
gnu: python-dendropy: Fix failing tests. 
* gnu/packages/patches/python-dendropy-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch.
 2017-02-24 23:44:31 +01:00
Marius Bakke 424b1ae769
Merge branch 'master' into python-tests 2017-02-13 22:35:05 +01:00
Ben Woodcroft 206af46fe1
gnu: vsearch: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0.
[source]: Convert most operations in the snippet to patch form and adjust
for 2.4.0.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-02-09 21:21:29 +10:00
Ricardo Wurmus 47055b273a
gnu: r-edger: Add r-statmod to inputs. 
* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
 2017-02-01 22:12:01 +01:00
Tobias Geerinckx-Rice 58f91e4d03
download: url-fetch/tarball: Make ‘name’ truly optional. 
* guix/download.scm (url-fetch/tarbomb): Fall back to ‘file-name’ if
‘name’ is #f, like the regular ‘url-fetch’ does.
* gnu/packages/bioinformatics.scm (muscle)[source]: Remove ‘file-name’.
* gnu/packages/engineering.scm (fastcap)[source]: Likewise.
* gnu/packages/scheme.scm (scmutils)[source]: Likewise.
 2017-02-01 15:53:32 +01:00
Raoul Jean Pierre Bonnal 69f2b3bdf9
gnu: Add r-rhdf5. 2017-01-31 22:35:11 +01:00
Raoul Jean Pierre Bonnal d4af25b51b
gnu: Add r-tximport. 2017-01-31 22:35:08 +01:00
Roel Janssen aa3eeeb542
gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
  New variable.
 2017-01-30 12:11:04 +01:00
Ben Woodcroft c0dee46c85
gnu: r-vegan: Update to 2.4-2. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
 2017-01-21 18:17:16 +10:00
Ben Woodcroft cda0f9a4a9
gnu: diamond: Update to 0.8.34. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
 2017-01-21 17:28:11 +10:00
Ricardo Wurmus 2923f3e5b9
gnu: r-msnid: Expand abbreviation in description. 
* gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS"
to "tandem mass spectrometry".
 2017-01-20 15:38:03 +01:00
Ricardo Wurmus e614d6398a
gnu: r-msnbase: Expand abbreviation in description. 
* gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS"
to "mass spectrometry".
 2017-01-20 15:38:03 +01:00
Ricardo Wurmus 1778ea740e
gnu: multiqc: Add python-nose to inputs. 
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add
python-nose.
 2017-01-18 16:09:49 +01:00
Ricardo Wurmus 66da3a9f31
gnu: Add r-msnid. 
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 11879284cb
gnu: Add r-msnbase. 
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 6a67e181ac
gnu: Add r-pcamethods. 
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 4aa7d592f1
gnu: Add r-mzid. 
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 7c08afaf7b
gnu: Add r-vsn. 
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 05c7e5fb76
gnu: Add r-affy. 
* gnu/packages/bioinformatics.scm (r-affy): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 5c9d15055f
gnu: Add r-affyio. 
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 71676a1f4c
gnu: Add r-mzr. 
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus ae26217430
gnu: Add r-protgenerics. 
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 0e7d058e44
gnu: Add r-maldiquant. 
* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 1f40e73cb5
gnu: Add r-raremetals2. 
* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus fb1e528ef1
gnu: Add r-seqminer. 
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus 769fc6bb18
gnu: Add ribodiff. 
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus e84efc50d7
gnu: Add hisat2. 
* gnu/packages/bioinformatics.scm (hisat2): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus b91cfa22e1
gnu: Add r-centipede. 
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
 2017-01-16 23:18:27 +01:00
Raoul Jean Pierre Bonnal dd42a330d1
gnu: Add r-sva. 
* gnu/packages/bioinformatics.scm (r-sva): New variable.
 2017-01-14 11:15:18 +01:00
Leo Famulari cc0725914e
Merge branch 'master' into python-tests 2017-01-13 10:21:17 -05:00
Roel Janssen c5173d74d6
gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene. 
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
 2017-01-12 10:02:57 +01:00
Ricardo Wurmus 3a3bf2f819
gnu: Add r-copywriter. 
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
 2017-01-06 16:31:19 +01:00
Ricardo Wurmus d407bdb931
gnu: Add r-copyhelper. 
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
 2017-01-06 16:31:14 +01:00
Ricardo Wurmus 6193563a36
gnu: Add r-chipseq. 
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
 2017-01-06 16:31:02 +01:00
Ben J Woodcroft dbf9d37114
gnu: bioruby: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
 2017-01-06 19:06:07 +10:00
Ben J Woodcroft 0c37e2a3d2
gnu: cd-hit: Update to 4.6.6. 
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
 2017-01-06 19:06:03 +10:00
Tobias Geerinckx-Rice 3b3b60d037
gnu: Use HTTPS for all sourceforge.net home pages. 
* gnu/packages/admin.scm (mingetty, clusterssh)[home-page]: Use HTTPS.
* gnu/packages/audio.scm (libbs2b, soxr)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (bless)[home-page]: Likewise.
* gnu/packages/display-managers.scm (slim)[home-page]: Likewise.
* gnu/packages/games.scm (extremetuxracer)[home-page]: Likewise.
* gnu/packages/ghostscript.scm (gs-fonts)[home-page]: Likewise.
* gnu/packages/haskell.scm (ghc-regex-base, ghc-regex-posix,
ghc-regex-compat)[home-page]: Likewise.
* gnu/packages/image.scm (imlib2)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (librevenge, libcmis, libodfgen, libmwaw)
[home-page]: Likewise.
* gnu/packages/linux.scm (hdparm, acpid, libavc1394, rng-tools)
[home-page]: Likewise.
* gnu/packages/mail.scm (esmtp)[home-page]: Likewise.
* gnu/packages/mp3.scm (ripperx)[home-page]: Likewise.
* gnu/packages/onc-rpc.scm (libtirpc)[home-page]: Likewise.
* gnu/packages/perl.scm (perl-czplib)[home-page]: Likewise.
* gnu/packages/python.scm (python-pyasn1-modules)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (xosd)[home-page]: Likewise.
 2017-01-04 05:14:22 +01:00
Roel Janssen 407a280103
gnu: r-genomicranges: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
 2017-01-03 13:28:35 +01:00
Roel Janssen ac370a3397
gnu: r-genomeinfodb: Update to 1.10.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
 2017-01-03 12:47:36 +01:00
Ben Woodcroft 25d84d3122
gnu: python-dendropy: Update to 4.2.0. 
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0.
[source]: Remove patch.
(python2-dendropy)[source]: Use the same source as python-dendropy.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-01-01 16:47:47 +10:00
Ben Woodcroft 322a583fcf
gnu: diamond: Update to 0.8.31. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
 2017-01-01 16:47:47 +10:00
Ben Woodcroft a29929b32c
gnu: multiqc: Update to 0.9. 
Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>.

* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-12-30 17:22:43 +10:00
Ricardo Wurmus 76b64381cb
gnu: r-genomicfeatures: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
 2016-12-29 22:24:12 +01:00
Ricardo Wurmus 2f642e5229
gnu: r-biostrings: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 72c2693b9e
gnu: r-limma: Update to 3.30.7. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 5796af9981
gnu: r-variantannotation: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 5d3acc0b36
gnu: r-edger: Update to 3.16.5. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 81a17b61e7
gnu: r-genomeinfodb: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 54d9b568fc
gnu: r-iranges: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 86fc9c4a2c
gnu: r-s4vectors: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus c8ad8b6976
gnu: r-biocstyle: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus 007ee80277
gnu: r-deseq2: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus d0f0579e6f
gnu: r-annotate: Update to 1.52.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1.
[propagated-inputs]: Add r-rcurl.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus 421f7772b4
gnu: r-qtl: Update to 1.40-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
 2016-12-29 21:49:09 +01:00
Ricardo Wurmus 2c8d6c0be4
gnu: r-rcas: Update to 1.1.1. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
 2016-12-27 14:50:55 +01:00
Ben Woodcroft 9916ef8bb6
gnu: diamond: Update to 0.8.30. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
 2016-12-27 09:18:05 +10:00