| Age | Commit message (Expand) | Author |
|---|
| 2020-09-11 | gnu: r-absfiltergsea: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here...
* gnu/packages/cran.scm (r-absfiltergsea): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-diversitree: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-diversitree): Move from here...
* gnu/packages/cran.scm (r-diversitree): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-phangorn: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-phangorn): Move from here...
* gnu/packages/cran.scm (r-phangorn): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-seurat: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seurat): Move from here...
* gnu/packages/cran.scm (r-seurat): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-maldiquant: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here...
* gnu/packages/cran.scm (r-maldiquant): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-seqminer: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seqminer): Move from here...
* gnu/packages/cran.scm (r-seqminer): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-qtl2: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-qtl2): Move from here...
* gnu/packages/cran.scm (r-qtl2): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-qtl: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-qtl): Move from here...
* gnu/packages/cran.scm (r-qtl): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-10 | gnu: Move r-bisquerna....* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ...
* gnu/packages/cran.scm: ... here.
| Roel Janssen |
| 2020-09-09 | Revert "gnu: Add r-loomr."...This reverts commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea.
This package is not free software.
| Ricardo Wurmus |
| 2020-09-09 | gnu: Add r-bisquerna....* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
| Roel Janssen |
| 2020-09-09 | gnu: Add r-loomr....* gnu/packages/bioinformatics.scm (r-loomr): New variable.
| Roel Janssen |
| 2020-09-05 | gnu: seqmagick: Update to 0.8.0....* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
| Andreas Enge |
| 2020-08-30 | gnu: delly: Update to 0.8.3....* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3.
[inputs]: Order alphabetically.
| Efraim Flashner |
| 2020-08-27 | gnu: vcflib: Install pkgconfig file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom
'install phase to add vcflib.pc.
| Efraim Flashner |
| 2020-08-27 | gnu: vcflib: Use shared libraries....* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add
snippet to adjust files for new locations.
[inputs]: Add fastahack, smithwaterman, tabixpp, xz.
[native-inputs]: Add pkg-config. Remove the package-source of fastahack,
fsom, smithwaterman, tabixpp.
[arguments]: Remove make-flags. Add custom phase to add the output lib
directory to the rpath. Adjust custom 'unpack-submodule-sources for the
change in native-inputs. Adjust custom 'install phase to also install
libraries and headers.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
| Efraim Flashner |
| 2020-08-27 | gnu: fastahack: Install pkgconfig file....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom
'install phase to add fastahack.pc.
| Efraim Flashner |
| 2020-08-27 | gnu: fastahack: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to
build PIE objects. Add custom phase to build dynamic library. Adjust
custom 'install phase to install shared library and headers.
| Efraim Flashner |
| 2020-08-27 | gnu: smithwaterman: Install pkgconfig file....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust
custom 'install phase to add smithwaterman.pc file.
| Efraim Flashner |
| 2020-08-27 | gnu: smithwaterman: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom
phase to build PIE objects. Add custom 'build-dynamic phase to build
dynamic library. Adjust custom 'install phase to install shared library
and headers.
| Efraim Flashner |
| 2020-08-27 | gnu: tabixpp: Install pkgconfig file....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'install phase to add tabixpp.pc file.
| Efraim Flashner |
| 2020-08-27 | gnu: tabixpp: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'build phase to build shared library. Adjust custom 'install phase to
install libraries and header.
| Efraim Flashner |
| 2020-08-20 | gnu: r-complexheatmap: Update to 2.4.3....* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-gage: Update to 2.38.3....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-annotationhub: Update to 2.20.2....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-delayedarray: Update to 0.14.1....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-annotationdbi: Update to 1.50.3....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-biocviews: Update to 1.56.2....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
| Ricardo Wurmus |
| 2020-08-19 | gnu: pigx-chipseq: Update to 0.0.43....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
| Ricardo Wurmus |
| 2020-08-18 | gnu: bowtie1: Add missing Python input....Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
| Ricardo Wurmus |
| 2020-08-16 | gnu: pigx-bsseq: Update to 0.1.2....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2.
[inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
| Ricardo Wurmus |
| 2020-08-16 | gnu: pigx-scrnaseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| Ricardo Wurmus |
| 2020-08-16 | gnu: pigx-bsseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| Ricardo Wurmus |
| 2020-08-16 | gnu: pigx-chipseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| Ricardo Wurmus |
| 2020-08-16 | gnu: pigx-rnaseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| Ricardo Wurmus |
| 2020-08-16 | gnu: r-rcas: Use pandoc instead of ghc-pandoc....* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Replace
ghc-pandoc with pandoc.
| Ricardo Wurmus |
| 2020-08-15 | gnu: hisat2: Use pandoc instead of ghc-pandoc....* gnu/packages/bioinformatics.scm (hisat2)[native-inputs]: Replace ghc-pandoc
with pandoc.
| Ricardo Wurmus |
| 2020-08-12 | gnu: tophat: Hide default GCC....* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
| Ricardo Wurmus |
| 2020-08-12 | gnu: r-seurat: Update to 3.2.0....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.2.0.
[propagated-inputs]: Remove r-tsne; add r-jsonlite, r-miniui, r-shiny, r-spatstat, and r-tibble.
| Ricardo Wurmus |
| 2020-08-10 | gnu: Add phast....* gnu/packages/bioinformatics.scm (phast): New variable.
| Ricardo Wurmus |
| 2020-08-07 | gnu: clipper: Update to 2.0....* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.
[source]: Remove snippet.
[arguments]: Build with Python 3; remove phase "fix-typo", add phase
"make-files-writable".
[inputs]: Replace all Python 2 variants with Python 3 variants.
[native-inputs]: Add python-setuptools-git.
| Ricardo Wurmus |
| 2020-07-30 | gnu: paml: Fix build....* gnu/packages/bioinformatics.scm (paml)[snippet]: Fix permissions
before repacking the source tarball.
| Jakub Kądziołka |
| 2020-07-19 | gnu: r-rhdf5lib: Fix libsz substitution....This is a follow-up to commit b7f051db14fb485fcfa4917924eef186fb1b8c07 -
in the new version, some of the format strings being replaced gained
quotes. This commit fixes build of dependents of r-rhdf5lib, such as
r-hdf5array.
* gnu/packages/bioinformatics (r-rhdf5lib): Remove all instances of libsz.a.
| Jakub Kądziołka |
| 2020-07-16 | gnu: Use HTTPS for mdc-berlin.de home pages....* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq)
(pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS.
| Tobias Geerinckx-Rice |
| 2020-07-16 | gnu: Use HTTPS for biojava.org home pages....* gnu/packages/bioinformatics.scm (java-biojava-core)
(java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0)
(java-biojava-alignment-4.0)[home-page]: Use HTTPS.
| Tobias Geerinckx-Rice |
| 2020-07-16 | gnu: r-rhdf5lib: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
| Ricardo Wurmus |
| 2020-07-16 | gnu: r-qtl2: Update to 0.22-11....* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
| Ricardo Wurmus |
| 2020-07-16 | gnu: r-genomicfeatures: Update to 1.40.1....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
| Ricardo Wurmus |
| 2020-07-16 | gnu: r-summarizedexperiment: Update to 1.18.2....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
| Ricardo Wurmus |
| 2020-07-16 | gnu: r-delayedmatrixstats: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
| Ricardo Wurmus |
