| Age | Commit message (Expand) | Author |
|---|
| 2018-11-07 | gnu: mash: Fetch sources from git....* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: fio: Update to 3.11....* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
| Marius Bakke |
| 2018-11-07 | gnu: kaiju: Update to 1.6.3....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
| Ricardo Wurmus |
| 2018-11-07 | gnu: kaiju: Fetch sources from git....* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
| Ricardo Wurmus |
| 2018-11-07 | gnu: idr: Fetch sources from git....* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: java-htsjdk: Fetch sources from git....* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: hisat2: Use versioned source URL....* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
| Ricardo Wurmus |
| 2018-11-07 | gnu: grit: Update to 2.0.5....* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
| Ricardo Wurmus |
| 2018-11-07 | gnu: grit: Fetch sources from git....* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: gemma: Update to 0.98....* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
| Ricardo Wurmus |
| 2018-11-07 | gnu: gemma: Fetch sources from git....* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: clementine: Build with sqlite-with-column-metadata....* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Pierre Langlois |
| 2018-11-07 | gnu: fxtract: Fetch sources from git....* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ribodiff: Fetch sources from git....* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python-biom-format: Update to 2.1.7....* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
| Ricardo Wurmus |
| 2018-11-07 | gnu: python-biom-format: Fetch source from git....* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bioawk: Fetch sources from git....* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bedtools-2.18: Fetch sources from stable URL....* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
| Ricardo Wurmus |
| 2018-11-07 | gnu: bamtools: Fetch sources from git....* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | gnu: ngless: Install links to required tools....* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
| Ricardo Wurmus |
| 2018-11-07 | gnu: prodigal: Fetch sources from git....* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
| Ricardo Wurmus |
| 2018-11-07 | services: cuirass: Add 'ttl' configuration field....* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field.
(cuirass-shepherd-service): Honor it.
| Ludovic Courtès |
| 2018-11-07 | gnu: cuirass: Update to 0b40dca....* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
| Ludovic Courtès |
| 2018-11-07 | linux-initrd: Make sure 'build-initrd' can delete files....Fixes <https://bugs.gnu.org/33297>.
Reported by Mark H Weaver <mhw@netris.org>.
This fixes a regression introduced in
72dc64f8f720268930eed448abfc15d2a0eca3cf, which made files read-only.
* gnu/build/linux-initrd.scm (build-initrd): Call 'make-file-writable'
on all the files under contents/.
| Ludovic Courtès |
| 2018-11-07 | gnu: r-mzr: Update to 2.16.0....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-rhdf5lib: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-hdf5array: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-rhdf5: Update to 2.26.0....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-rcas: Update to 1.8.0....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-delayedmatrixstats: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-scran: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-scater: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-singlecellexperiment: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-beachmat: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-qvalue: Update to 2.14.0....* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-hitc: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-fithic: Update to 1.8.0....* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-sushi: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-gwascat: Update to 2.14.0....* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-gviz: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-gqtlstats: Update to 1.14.0....* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-ldblock: Update to 1.12.0....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-erma: Update to 0.14.0....* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-snpstats: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-gqtlbase: Update to 1.14.0....* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-ggbio: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-biovizbase: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-organismdbi: Update to 1.24.0....* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-ensembldb: Update to 2.6.0....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
| Ricardo Wurmus |
| 2018-11-07 | gnu: r-dirichletmultinomial: Update to 1.24.0....* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
| Ricardo Wurmus |
