| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| ... | |
| * | gnu: pyicoteo: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -5/+6 |
| * | gnu: hplip: Remove bundled non-free blobs.•••This fixes <https://bugs.gnu.org/32184>.
* gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to
remove non-free code and binary blobs.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
| Efraim Flashner | 2018-11-07 | 3 | -1/+238 |
| * | pull: Add missing monadic 'return'.•••Fixes a regression introduced in
5f7dd092ca577a534067f577b8849ed06cabf970 where, upon completion, 'guix
pull' would fail (instead of printing the new/upgraded packages) with
ugly errors like:
successfully built /gnu/store/…-profile.drv
1 package in profile
Backtrace:
[…]
In guix/store.scm:
1605:24 1 (run-with-store _ _ #:guile-for-build _ #:system _ # _)
In unknown file:
0 (_ #<build-daemon 256.97 2476b40>)
ERROR: Wrong type to apply: #t
Reported by thorwil on #guix.
* guix/scripts/pull.scm (build-and-install): Add missing 'return' when
DRY-RUN? is wrong.
| Ludovic Courtès | 2018-11-07 | 1 | -1/+1 |
| * | gnu: sra-tools: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | gnu: libgff: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | gnu: kentutils: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
| Ricardo Wurmus | 2018-11-07 | 1 | -5/+8 |
| * | gnu: r-seqgl: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -5/+6 |
| * | gnu: pplacer: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
| Ricardo Wurmus | 2018-11-07 | 1 | -7/+9 |
| * | gnu: minced: Update to 0.3.2.•••* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | gnu: minced: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | gnu: metabat: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -5/+6 |
| * | gnu: mash: Update to 2.1.•••* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | gnu: mash: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | 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 | 1 | -3/+3 |
| * | gnu: kaiju: Update to 1.6.3.•••* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | 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 | 1 | -8/+7 |
| * | gnu: idr: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | gnu: java-htsjdk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | gnu: hisat2: Use versioned source URL.•••* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
| Ricardo Wurmus | 2018-11-07 | 1 | -8/+3 |
| * | gnu: grit: Update to 2.0.5.•••* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
| Ricardo Wurmus | 2018-11-07 | 1 | -9/+3 |
| * | gnu: grit: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | 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 | 3 | -49/+15 |
| * | gnu: gemma: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -5/+6 |
| * | 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 | 1 | -1/+1 |
| * | gnu: fxtract: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -8/+6 |
| * | gnu: ribodiff: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -5/+6 |
| * | 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 | 1 | -3/+26 |
| * | gnu: python-biom-format: Fetch source from git.•••* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
| Ricardo Wurmus | 2018-11-07 | 1 | -29/+30 |
| * | gnu: bioawk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -13/+15 |
| * | 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 | 1 | -3/+3 |
| * | gnu: bamtools: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | 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 | 1 | -2/+23 |
| * | gnu: prodigal: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
| Ricardo Wurmus | 2018-11-07 | 1 | -6/+6 |
| * | 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 | 2 | -1/+10 |
| * | gnu: cuirass: Update to 0b40dca.•••* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
| Ludovic Courtès | 2018-11-07 | 1 | -3/+3 |
| * | 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 | 1 | -1/+7 |
| * | 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 | 1 | -3/+3 |
| * | 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 | 1 | -5/+11 |
| * | gnu: r-hdf5array: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | gnu: r-rhdf5: Update to 2.26.0.•••* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | 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 | 1 | -14/+6 |
| * | 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 | 1 | -3/+5 |
| * | 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 | 1 | -8/+4 |
| * | 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 | 1 | -11/+3 |
| * | gnu: r-singlecellexperiment: Update to 1.4.0.•••* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | 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 | 1 | -3/+4 |
| * | gnu: r-qvalue: Update to 2.14.0.•••* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | gnu: r-hitc: Update to 1.26.0.•••* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | gnu: r-fithic: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
| * | gnu: r-sushi: Update to 1.20.0.•••* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
| Ricardo Wurmus | 2018-11-07 | 1 | -2/+2 |
