| Age | Commit message (Expand) | Author |
|---|
| 2017-03-30 | 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 | gnu: stringtie: Remove typedef conflict....* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting
typedef in a new build phase "remove-duplicate-typedef".
| Ricardo Wurmus |
| 2017-03-23 | gnu: star: Update to 2.5.3a....* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
| Ricardo Wurmus |
| 2017-03-22 | gnu: python-pysam: Run tests in parallel....* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
| Ricardo Wurmus |
| 2017-03-22 | 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 | gnu: python-pysam: Update to 0.10.0....* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
| Ricardo Wurmus |
| 2017-03-19 | 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 |
| 2017-03-17 | 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 | 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 |
| 2017-03-16 | 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 | 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 | gnu: ncbi-vdb: Install configuration files....* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
| Ricardo Wurmus |
| 2017-03-16 | 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 | gnu: ncbi-vdb: Use modify-phases syntax....* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
| Ricardo Wurmus |
| 2017-03-16 | gnu: ncbi-vdb: Update to 2.8.2....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
| Ricardo Wurmus |
| 2017-03-16 | gnu: ngs-sdk: Update to 1.3.0....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
| Ricardo Wurmus |
| 2017-03-15 | 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 | 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 |
| 2017-03-11 | gnu: vsearch: Update to 2.4.2....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
| Ben Woodcroft |
| 2017-03-11 | gnu: Add r-ape....* gnu/packages/bioinformatics.scm (r-ape): New variable.
Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
| Raoul Jean Pierre Bonnal |
| 2017-03-10 | gnu: hmmer: Build reproducibly....* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.
| Ben J. Woodcroft |
| 2017-03-10 | gnu: Add sambamba....* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
| Ricardo Wurmus |
| 2017-03-03 | Merge branch 'python-tests' | Marius Bakke |
| 2017-03-02 | gnu: diamond: Update to 0.8.36....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
| Ben Woodcroft |
| 2017-02-28 | gnu: bamtools: Update to 2.4.1....* gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
| Ricardo Wurmus |
| 2017-02-27 | gnu: ribodiff: Fix test failure....* gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK
and PYTHON2-NOSE.
| Marius Bakke |
| 2017-02-24 | 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.
| Ricardo Wurmus |
| 2017-02-13 | Merge branch 'master' into python-tests | Marius Bakke |
| 2017-02-09 | 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.
| Ben Woodcroft |
| 2017-02-01 | gnu: r-edger: Add r-statmod to inputs....* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
| Ricardo Wurmus |
| 2017-02-01 | 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.
| Tobias Geerinckx-Rice |
| 2017-01-31 | gnu: Add r-rhdf5. | Raoul Jean Pierre Bonnal |
| 2017-01-31 | gnu: Add r-tximport. | Raoul Jean Pierre Bonnal |
| 2017-01-30 | gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5....* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
New variable.
| Roel Janssen |
| 2017-01-21 | gnu: r-vegan: Update to 2.4-2....* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
| Ben Woodcroft |
| 2017-01-21 | gnu: diamond: Update to 0.8.34....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
| Ben Woodcroft |
| 2017-01-20 | gnu: r-msnid: Expand abbreviation in description....* gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS"
to "tandem mass spectrometry".
| Ricardo Wurmus |
| 2017-01-20 | gnu: r-msnbase: Expand abbreviation in description....* gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS"
to "mass spectrometry".
| Ricardo Wurmus |
| 2017-01-18 | gnu: multiqc: Add python-nose to inputs....* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add
python-nose.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-msnid....* gnu/packages/bioinformatics.scm (r-msnid): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-msnbase....* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-pcamethods....* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-mzid....* gnu/packages/bioinformatics.scm (r-mzid): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-vsn....* gnu/packages/bioinformatics.scm (r-vsn): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-affy....* gnu/packages/bioinformatics.scm (r-affy): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-affyio....* gnu/packages/bioinformatics.scm (r-affyio): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-mzr....* gnu/packages/bioinformatics.scm (r-mzr): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-protgenerics....* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-maldiquant....* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
| Ricardo Wurmus |
| 2017-01-17 | gnu: Add r-raremetals2....* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
| Ricardo Wurmus |
