| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: raxml: Update to 8.2.10.•••* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.10.
| Ben Woodcroft | 2017-04-09 | 1 | -2/+2 |
| * | gnu: r-rsamtools: Update to 1.26.2.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.2.
| Ricardo Wurmus | 2017-04-09 | 1 | -2/+2 |
| * | gnu: r-biocparallel: Update to 1.8.2.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.2.
| Ricardo Wurmus | 2017-04-09 | 1 | -2/+2 |
| * | 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".
| Ricardo Wurmus | 2017-04-08 | 1 | -25/+3 |
| * | gnu: vsearch: Update to 2.4.3.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
| Ben Woodcroft | 2017-04-07 | 1 | -2/+2 |
| * | gnu: r-seqinr: Update to 3.3-6.•••* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | 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.
| Ricardo Wurmus | 2017-04-06 | 1 | -8/+0 |
| * | gnu: r-annotationforge: Update to 1.16.1.•••* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-shortread: Update to 1.32.1.•••* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-s4vectors: Update to 0.12.2.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-iranges: Update to 2.8.2.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-variantannotation: Update to 1.20.3.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-limma: Update to 3.30.13.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-genomicranges: Update to 1.26.4.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-annotationdbi: Update to 1.36.2.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-genomicalignments: Update to 1.10.1.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-rtracklayer: Update to 1.34.2.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-genomicfeatures: Update to 1.26.4.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-seqminer: Update to 5.7.•••* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-maldiquant: Update to 1.16.2.•••* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | gnu: r-genomeinfodb: Update to 1.10.3.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3.
[propagated-inputs]: Add "r-rcurl".
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+3 |
| * | gnu: r-xvector: Update to 0.14.1.•••* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
| Ricardo Wurmus | 2017-04-06 | 1 | -2/+2 |
| * | 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".
| Ricardo Wurmus | 2017-04-06 | 1 | -4/+2 |
| * | 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.
| Ricardo Wurmus | 2017-04-05 | 1 | -1/+13 |
| * | gnu: sra-tools: Use "modify-phases" syntax.•••* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
| Ricardo Wurmus | 2017-04-05 | 1 | -44/+43 |
| * | gnu: diamond: Update to 0.8.37.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
| Ben Woodcroft | 2017-04-05 | 1 | -2/+2 |
| * | 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.
| Leo Famulari | 2017-04-02 | 1 | -4/+4 |
| * | gnu: khmer: Build with gcc-4.•••* gnu/packages/bioinformatics.scm (khmer)[inputs]: Add gcc-4.9.
| Ben Woodcroft | 2017-04-02 | 1 | -1/+4 |
| * | Merge branch 'master' into core-updates•••Most conflicts are from 6fd52309b8f52c9bb59fccffac53e029ce94b698.
| Marius Bakke | 2017-03-30 | 1 | -1/+1 |
| |\ |
|
| | * | 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) ...)'.
| Ludovic Courtès | 2017-03-28 | 1 | -1/+1 |
| * | | gnu: discrover: Add missing includes.•••* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"add-missing-includes" to include "random" headers.
| Ricardo Wurmus | 2017-03-30 | 1 | -1/+13 |
| * | | gnu: stringtie: Remove typedef conflict.•••* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting
typedef in a new build phase "remove-duplicate-typedef".
| Ricardo Wurmus | 2017-03-30 | 1 | -0/+7 |
| |/ |
|
| * | gnu: star: Update to 2.5.3a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
| Ricardo Wurmus | 2017-03-23 | 1 | -2/+2 |
| * | gnu: python-pysam: Run tests in parallel.•••* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
| Ricardo Wurmus | 2017-03-22 | 1 | -1/+3 |
| * | gnu: python-pysam: Run tests before installation.•••* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
| Ricardo Wurmus | 2017-03-22 | 1 | -13/+15 |
| * | gnu: python-pysam: Update to 0.10.0.•••* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
| Ricardo Wurmus | 2017-03-22 | 1 | -2/+2 |
| * | 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".
| Ludovic Courtès | 2017-03-19 | 1 | -1/+1 |
| * | 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".
| Ricardo Wurmus | 2017-03-17 | 1 | -5/+5 |
| * | 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.
| Ricardo Wurmus | 2017-03-17 | 1 | -4/+17 |
| * | gnu: Add r-seurat.•••* gnu/packages/bioinformatics.scm (r-seurat): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Raoul Jean Pierre Bonnal | 2017-03-16 | 1 | -0/+79 |
| * | 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.
| Ricardo Wurmus | 2017-03-16 | 1 | -3/+9 |
| * | gnu: ncbi-vdb: Install configuration files.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
| Ricardo Wurmus | 2017-03-16 | 1 | -0/+8 |
| * | 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".
| Ricardo Wurmus | 2017-03-16 | 1 | -2/+5 |
| * | gnu: ncbi-vdb: Use modify-phases syntax.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
| Ricardo Wurmus | 2017-03-16 | 1 | -55/+54 |
| * | gnu: ncbi-vdb: Update to 2.8.2.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
| Ricardo Wurmus | 2017-03-16 | 1 | -2/+2 |
| * | gnu: ngs-sdk: Update to 1.3.0.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
| Ricardo Wurmus | 2017-03-16 | 1 | -2/+2 |
| * | 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.
| Tobias Geerinckx-Rice | 2017-03-15 | 1 | -23/+14 |
| * | 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.
| Tobias Geerinckx-Rice | 2017-03-15 | 1 | -2/+4 |
| * | gnu: vsearch: Update to 2.4.2.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
| Ben Woodcroft | 2017-03-11 | 1 | -2/+2 |
| * | gnu: Add r-ape.•••* gnu/packages/bioinformatics.scm (r-ape): New variable.
Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
| Raoul Jean Pierre Bonnal | 2017-03-11 | 1 | -0/+22 |
