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* gnu: Fix typos in descriptions.Tobias Geerinckx-Rice2017-04-17
| | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: mafft: Update to 7.310.Ben Woodcroft2017-04-14
| | | | * gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
* gnu: raxml: Update to 8.2.10.Ben Woodcroft2017-04-09
| | | | * gnu/packages/bioinformatics.scm (raxml): Update to 8.2.10.
* gnu: r-rsamtools: Update to 1.26.2.Ricardo Wurmus2017-04-09
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.2.
* gnu: r-biocparallel: Update to 1.8.2.Ricardo Wurmus2017-04-09
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.2.
* gnu: r-vegan: Update to 2.4-3.Ricardo Wurmus2017-04-08
| | | | | | * 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".
* gnu: vsearch: Update to 2.4.3.Ben Woodcroft2017-04-07
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
* gnu: r-seqinr: Update to 3.3-6.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
* gnu: r-rcpparmadillo: Update to 0.7.700.0.0.Ricardo Wurmus2017-04-06
| | | | | | | | | | | * 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.
* gnu: r-annotationforge: Update to 1.16.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
* gnu: r-shortread: Update to 1.32.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
* gnu: r-s4vectors: Update to 0.12.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
* gnu: r-iranges: Update to 2.8.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
* gnu: r-variantannotation: Update to 1.20.3.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
* gnu: r-limma: Update to 3.30.13.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
* gnu: r-genomicranges: Update to 1.26.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
* gnu: r-annotationdbi: Update to 1.36.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
* gnu: r-genomicalignments: Update to 1.10.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
* gnu: r-rtracklayer: Update to 1.34.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
* gnu: r-genomicfeatures: Update to 1.26.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
* gnu: r-seqminer: Update to 5.7.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
* gnu: r-maldiquant: Update to 1.16.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
* gnu: r-genomeinfodb: Update to 1.10.3.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3. [propagated-inputs]: Add "r-rcurl".
* gnu: r-xvector: Update to 0.14.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
* gnu: r-bioccheck: Update to 1.10.1.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1. [propagated-inputs]: Remove "r-knitr" and "r-devtools".
* gnu: sra-tools: Fix glibc naming conflict.Ricardo Wurmus2017-04-05
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase "patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
* gnu: sra-tools: Use "modify-phases" syntax.Ricardo Wurmus2017-04-05
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases" syntax.
* gnu: diamond: Update to 0.8.37.Ben Woodcroft2017-04-05
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
* gnu: Use HTTPS URLs for GitHub home-pages.Leo Famulari2017-04-02
| | | | | | | | | * 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.
* gnu: khmer: Build with gcc-4.Ben Woodcroft2017-04-02
| | | | * gnu/packages/bioinformatics.scm (khmer)[inputs]: Add gcc-4.9.
* Merge branch 'master' into core-updatesMarius Bakke2017-03-30
|\ | | | | | | Most conflicts are from 6fd52309b8f52c9bb59fccffac53e029ce94b698.
| * Replace (compose not PROC) with simpler idioms.Ludovic Courtès2017-03-28
| | | | | | | | | | | | | | | | * 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) ...)'.
* | gnu: discrover: Add missing includes.Ricardo Wurmus2017-03-30
| | | | | | | | | | * gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase "add-missing-includes" to include "random" headers.
* | gnu: stringtie: Remove typedef conflict.Ricardo Wurmus2017-03-30
|/ | | | | * gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting typedef in a new build phase "remove-duplicate-typedef".
* gnu: star: Update to 2.5.3a.Ricardo Wurmus2017-03-23
| | | | * gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
* gnu: python-pysam: Run tests in parallel.Ricardo Wurmus2017-03-22
| | | | | * gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in parallel.
* gnu: python-pysam: Run tests before installation.Ricardo Wurmus2017-03-22
| | | | | * gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check phase to be run before installation.
* gnu: python-pysam: Update to 0.10.0.Ricardo Wurmus2017-03-22
| | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
* gnu: Rename "guile-next" to "guile".Ludovic Courtès2017-03-19
| | | | | | | | | | | | | | * 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".
* gnu: r: Rename to r-minimal.Ricardo Wurmus2017-03-17
| | | | | | | | | | | | | | | | * 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".
* gnu: r: Do not build recommended packages.Ricardo Wurmus2017-03-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: Add r-seurat.Raoul Jean Pierre Bonnal2017-03-16
| | | | | | * gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: sra-tools: Update to 2.8.2-1.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
* gnu: ncbi-vdb: Install configuration files.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files".
* gnu: ncbi-vdb: Override search path for java-ngs.Ricardo Wurmus2017-03-16
| | | | | | * 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".
* gnu: ncbi-vdb: Use modify-phases syntax.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax.
* gnu: ncbi-vdb: Update to 2.8.2.Ricardo Wurmus2017-03-16
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
* gnu: ngs-sdk: Update to 1.3.0.Ricardo Wurmus2017-03-16
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
* gnu: Use INSTALL-FILE where appropriate.Tobias Geerinckx-Rice2017-03-15
| | | | | | | | | | | | * 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.
* gnu: samtools: End installation phases with truth.Tobias Geerinckx-Rice2017-03-15
| | | | | * gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
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