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2017-03-30Merge branch 'master' into core-updatesMarius Bakke
Most conflicts are from 6fd52309b8f52c9bb59fccffac53e029ce94b698.
2017-03-30gnu: discrover: Add missing includes.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase "add-missing-includes" to include "random" headers.
2017-03-30gnu: stringtie: Remove typedef conflict.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting typedef in a new build phase "remove-duplicate-typedef".
2017-03-28Replace (compose not PROC) with simpler idioms.Ludovic Courtès
* 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) ...)'.
2017-03-23gnu: star: Update to 2.5.3a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
2017-03-22gnu: python-pysam: Run tests in parallel.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in parallel.
2017-03-22gnu: python-pysam: Run tests before installation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check phase to be run before installation.
2017-03-22gnu: python-pysam: Update to 0.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
2017-03-19gnu: Rename "guile-next" to "guile".Ludovic Courtès
* 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".
2017-03-17gnu: r: Rename to r-minimal.Ricardo Wurmus
* 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".
2017-03-17gnu: r: Do not build recommended packages.Ricardo Wurmus
* 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.
2017-03-16gnu: Add r-seurat.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-03-16gnu: sra-tools: Update to 2.8.2-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
2017-03-16gnu: ncbi-vdb: Install configuration files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files".
2017-03-16gnu: ncbi-vdb: Override search path for java-ngs.Ricardo Wurmus
* 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".
2017-03-16gnu: ncbi-vdb: Use modify-phases syntax.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax.
2017-03-16gnu: ncbi-vdb: Update to 2.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
2017-03-16gnu: ngs-sdk: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
2017-03-15gnu: Use INSTALL-FILE where appropriate.Tobias Geerinckx-Rice
* 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.
2017-03-15gnu: samtools: End installation phases with truth.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
2017-03-11gnu: vsearch: Update to 2.4.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
2017-03-11gnu: Add r-ape.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-ape): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-10gnu: hmmer: Build reproducibly.Ben J. Woodcroft
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file. * gnu/packages/bioinformatics.scm (hmmer): Use it.
2017-03-10gnu: Add sambamba.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New variables.
2017-03-03Merge branch 'python-tests'Marius Bakke
2017-03-02gnu: diamond: Update to 0.8.36.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
2017-02-28gnu: bamtools: Update to 2.4.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
2017-02-27gnu: ribodiff: Fix test failure.Marius Bakke
* gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK and PYTHON2-NOSE.
2017-02-24gnu: python-dendropy: Fix failing tests.Ricardo Wurmus
* 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.
2017-02-13Merge branch 'master' into python-testsMarius Bakke
2017-02-09gnu: vsearch: Update to 2.4.0.Ben Woodcroft
* 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.
2017-02-01gnu: r-edger: Add r-statmod to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
2017-02-01download: url-fetch/tarball: Make ‘name’ truly optional.Tobias Geerinckx-Rice
* 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.
2017-01-31gnu: Add r-rhdf5.Raoul Jean Pierre Bonnal
2017-01-31gnu: Add r-tximport.Raoul Jean Pierre Bonnal
2017-01-30gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): New variable.
2017-01-21gnu: r-vegan: Update to 2.4-2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
2017-01-21gnu: diamond: Update to 0.8.34.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
2017-01-20gnu: r-msnid: Expand abbreviation in description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS" to "tandem mass spectrometry".
2017-01-20gnu: r-msnbase: Expand abbreviation in description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS" to "mass spectrometry".
2017-01-18gnu: multiqc: Add python-nose to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add python-nose.
2017-01-17gnu: Add r-msnid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
2017-01-17gnu: Add r-msnbase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
2017-01-17gnu: Add r-pcamethods.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
2017-01-17gnu: Add r-mzid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
2017-01-17gnu: Add r-vsn.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
2017-01-17gnu: Add r-affy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-affy): New variable.
2017-01-17gnu: Add r-affyio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
2017-01-17gnu: Add r-mzr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
2017-01-17gnu: Add r-protgenerics.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
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