88eb119f95
gnu: mafft: Update to 7.310.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
2017-04-14 15:19:37 +10:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
84157bb8bf
Merge branch 'master' into core-updates
...
Most conflicts are from 6fd52309b8
2017-03-30 22:59:53 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
5ded35d89d
gnu: Add sambamba.
...
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
2017-03-10 10:13:59 +01:00
3f98071ac5
Merge branch 'python-tests'
2017-03-03 16:55:43 +01:00
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
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
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
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
424b1ae769
Merge branch 'master' into python-tests
2017-02-13 22:35:05 +01:00
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
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
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
69f2b3bdf9
gnu: Add r-rhdf5.
2017-01-31 22:35:11 +01:00
d4af25b51b
gnu: Add r-tximport.
2017-01-31 22:35:08 +01:00
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
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
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
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
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
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
66da3a9f31
gnu: Add r-msnid.
...
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
2017-01-17 21:46:50 +01:00
11879284cb
gnu: Add r-msnbase.
...
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
2017-01-17 21:46:50 +01:00
6a67e181ac
gnu: Add r-pcamethods.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
2017-01-17 21:46:50 +01:00
4aa7d592f1
gnu: Add r-mzid.
...
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
2017-01-17 21:46:50 +01:00
7c08afaf7b
gnu: Add r-vsn.
...
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
2017-01-17 21:46:50 +01:00
05c7e5fb76
gnu: Add r-affy.
...
* gnu/packages/bioinformatics.scm (r-affy): New variable.
2017-01-17 21:46:49 +01:00
5c9d15055f
gnu: Add r-affyio.
...
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
2017-01-17 21:46:49 +01:00
71676a1f4c
gnu: Add r-mzr.
...
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
2017-01-17 21:46:49 +01:00
ae26217430
gnu: Add r-protgenerics.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
2017-01-17 21:46:49 +01:00
0e7d058e44
gnu: Add r-maldiquant.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
2017-01-17 21:46:49 +01:00
1f40e73cb5
gnu: Add r-raremetals2.
...
* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
2017-01-17 21:46:48 +01:00
fb1e528ef1
gnu: Add r-seqminer.
...
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
2017-01-17 21:46:48 +01:00
769fc6bb18
gnu: Add ribodiff.
...
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
2017-01-17 21:46:48 +01:00
e84efc50d7
gnu: Add hisat2.
...
* gnu/packages/bioinformatics.scm (hisat2): New variable.
2017-01-17 21:46:48 +01:00
b91cfa22e1
gnu: Add r-centipede.
...
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
2017-01-16 23:18:27 +01:00
dd42a330d1
gnu: Add r-sva.
...
* gnu/packages/bioinformatics.scm (r-sva): New variable.
2017-01-14 11:15:18 +01:00
cc0725914e
Merge branch 'master' into python-tests
2017-01-13 10:21:17 -05:00
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
3a3bf2f819
gnu: Add r-copywriter.
...
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
2017-01-06 16:31:19 +01:00
d407bdb931
gnu: Add r-copyhelper.
...
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
2017-01-06 16:31:14 +01:00
6193563a36
gnu: Add r-chipseq.
...
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
2017-01-06 16:31:02 +01:00
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
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
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
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
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
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
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
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
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
2f642e5229
gnu: r-biostrings: Update to 2.42.1.
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* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
2016-12-29 22:24:11 +01:00
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
5796af9981
gnu: r-variantannotation: Update to 1.20.2.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
2016-12-29 22:24:11 +01:00
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
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
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
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
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
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
d0f0579e6f
gnu: r-annotate: Update to 1.52.1.
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* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1.
[propagated-inputs]: Add r-rcurl.
2016-12-29 22:24:10 +01:00
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
2c8d6c0be4
gnu: r-rcas: Update to 1.1.1.
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* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
2016-12-27 14:50:55 +01:00
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
33d5b2464d
gnu: cutadapt: Use ‘modify-phases’ syntax.
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* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
2016-12-20 05:36:55 +01:00
1f94bff2d4
gnu: cutadapt: Update to 1.12.
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* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12.
[inputs]: Add python-xopen.
2016-12-19 20:33:32 +01:00
3fffabce2a
gnu: Add attribution line for Raoul Bonnal.
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This is a follow-up commit to c9e9154e99
2016-12-18 10:01:04 +10:00
c9e9154e99
gnu: star: Update to 2.5.2b.
...
* gnu/packages/bioinformatics (star): Update to 2.5.2b.
[source]: Delete precompiled binary.
Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2016-12-17 23:26:35 +10:00
cdc2bb50b2
gnu: pbtranscript-tofu: Disable tests.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
2016-12-16 18:15:47 +01:00
0d90875974
gnu: multiqc: Fix test dependencies.
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* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
2016-12-16 13:28:49 +01:00
14386fc7d9
gnu: idr: Remove explicit wrapper. This is now done implicitly.
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* gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases.
2016-12-16 13:16:39 +01:00
b7a820fc97
gnu: idr: Correct inputs.
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* gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ...
[propagated-inputs]: ... to here. Add python-sympy.
2016-12-16 13:11:20 +01:00
1c10a1d75c
gnu: idr: Disable tests.
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* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
2016-12-16 13:08:57 +01:00
aaffb9c97b
gnu: deeptools: Fix test dependency.
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* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
2016-12-16 04:27:35 +01:00
d281be18bc
gnu: clipper: Fix test dependency.
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* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
2016-12-16 04:26:32 +01:00
0c6c9c00ab
gnu: Update more dead Google Code home pages.
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* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
2016-12-14 22:08:51 +01:00
da5ebd1007
gnu: python-biom-format: Fix tests.
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* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format)[native-inputs]: Add python-nose.
2016-12-14 19:18:26 +01:00
991e143d25
gnu: diamond: Update to 0.8.29.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
2016-12-13 20:01:56 +10:00
ced1c496aa
gnu: orfm: Update to 0.6.1.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
2016-12-13 20:00:50 +10:00
2df3d147ef
gnu: orfm: Update to 0.6.0.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
2016-12-12 20:49:31 +10:00
a225db5293
gnu: vsearch: Update to 2.3.4.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
2016-12-10 10:45:13 +10:00
7922ab8fe8
gnu: pardre: Update to 1.1.5-1.
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* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
2016-12-10 10:45:12 +10:00
1b7f17ef90
gnu: vsearch: Update to 2.3.3.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
2016-12-08 22:39:10 +10:00
e990c81d38
gnu: aragorn: Update to 1.2.38.
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* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
2016-12-04 10:51:54 +10:00
3bf4280659
Merge branch 'master' into python-build-system
2016-11-29 18:47:16 +01:00
bd3be46e7f
gnu: Add r-gkmsvm.
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* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
2016-11-28 22:43:18 +01:00
2d9fb1702f
gnu: Add r-seqgl.
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* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
2016-11-28 22:43:17 +01:00
c827f20286
gnu: Add r-chipkernels.
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* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
2016-11-28 22:43:17 +01:00
d71605294f
gnu: Add r-wgcna.
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* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
2016-11-28 22:43:17 +01:00
e619a5c245
gnu: Add r-r4rna.
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* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
2016-11-28 22:43:16 +01:00
9926875572
gnu: Add newick-utils.
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* gnu/packages/bioinformatics.scm (newick-utils): New variable.
2016-11-28 09:00:41 +10:00
5e0a0f4226
gnu: roary: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
2016-11-26 20:15:39 +10:00
31a9d653ad
gnu: Add proteinortho.
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* gnu/packages/bioinformatics.scm (proteinortho): New variable.
2016-11-26 20:15:37 +10:00
de32aa74b4
Merge branch 'master' into python-build-system
2016-11-25 11:20:21 -05:00
8e5f8c98e2
gnu: diamond: Update to 0.8.27.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
2016-11-22 21:01:21 +10:00
daf72603eb
gnu: Remove redundancy where mkdir-p <dir> is followed by install-file <file> <dir>.
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* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p.
(eigensoft)[arguments]: Likewise.
(snap-aligner)[arguments]: Likewise.
(pardre)[arguments]: Likewise.
(piranha)[arguments]: Likewise.
* gnu/packages/maths.scm (hypre)[arguments]: Likewise.
* gnu/packages/mp3.scm (mpc123)[arguments]: Likewise.
* gnu/packages/music.scm (tuxguitar)[arguments]: Likewise.
* gnu/packages/pdf.scm (impressive)[arguments]: Likewise.
* gnu/packages/qemu.scm (qemu)[arguments]: Likewise.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-11-21 14:39:54 -05:00
de5bc89093
gnu: python2-pbcore: Fix inputs:
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* gnu/packages/bioinformatics.scm (python2-pbcore) [inputs] change to
[propagated-inputs]. [native-inputs]: Remove python-docutils, which
comes with sphinx. [former propagated-inputs]: move all (which is only
pyxb) to [inputs].
2016-11-15 22:32:01 +01:00
54c85e12fd
gnu: python2-warpedlmm: Remove phase remove-bin-directory.
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This directory did contain contain wrappers for `nose`, which should not
be there anyway (since nose already was a native-input). The new
python build system no longer creates this directory, while the old one
did. (This difference is due to the bloody details of how packages are
installed.)
* gnu/packages/bioinformatics.scm (python2-warpedlmm)
[modify-phases] Remove, since remove-bin-directory was the only
modification here.
2016-11-15 22:32:00 +01:00
f2516de2fc
gnu: Fix python inputs, part 7: Ensure python-cython is a native-input.
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* gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to
[native-inputs].
* gnu/packages/bioinformatics.scm (python2-pybedtools): dito.
* gnu/packages/music.scm (beast, python-pyportmidi): dito.
* gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.
2016-11-15 22:31:07 +01:00
f22efa0152
gnu: Fix python inputs, part 1: all inputs become propagated-inputs.
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This patch contains the changes where all [inputs] are changed to
[propagated-inputs]
* gnu/packages/python.scm (python-passlib, python-paramiko, python-ccm,
python-babel, python-keyring python-pandas, python-tzlocal,
python-parse-type, python-nose2, python-pytest, python-pytest-mock,
python-pytest-xdist, python-scripttest, python-testtools, python-pytest-cov,
python-testscenarios, python-pbr-0.11, python-oauthlib, python-jinja2,
python-sphinx, python-tzlocal, python-bugz, python2-pytest-mock, behave,
pelican, sqlalchemy-utils, python-pygridtools, python-urwidtrees,
python-tornado, python2-tornado, python-debian, python-execnet,
python-pytest-cache, pytest-localserver, python-clint, python-rply,
python-hy, python-rauth, python-rsa, python-celery, python-vobject, s3cmd,
python-prompt-toolkit, ptpython, python-requests-oauthlib, python-stem,
python-binaryornot, python2-binaryornot, python-nltk, python-pymongo,
python-schematics, python-url, python2-url, python-freezegun,
python-glances, python-graphql-core, python-graphql-relay, python-graphene,
python-nautilus, python-s3transfer): All [inputs] become
[propagated-inputs].
* gnu/packages/bioinformatics.scm (python-biopython): Likewise.
* gnu/packages/django.scm (pytest-django): Likewise.
* gnu/packages/mail.scm (python-mailmanclient): Likewise.
* gnu/packages/password-utils.scm (python-bcrypt): Likewise.
* gnu/packages/propbuf.scm (python-protobuf): Likewise.
* gnu/packages/rdf.scm (python-rdflib): Likewise.
SQACH all become propagated
2016-11-15 22:31:03 +01:00
b41a05ce49
gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).
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Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
configure-flags. (python-pillow) remove phase
"disable-egg-generation". (python-libarchive-c) Remove patching
setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
"prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
"disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
2016-11-15 22:31:02 +01:00
Ben Woodcroft