| Age | Commit message (Expand) | Author |
|---|
| 2019-04-03 | gnu: r-rcas: Add upstream name....* gnu/packages/bioinformatics.scm (r-rcas)[properties]: Add upstream name.
| Ricardo Wurmus |
| 2019-04-02 | gnu: pigx-scrnaseq: Use older loompy....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
python-loompy with python-loompy-for-pigx-scrnaseq.
| Ricardo Wurmus |
| 2019-04-02 | gnu: Add python-loompy-for-pigx-scrnaseq....* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): New variable.
| Ricardo Wurmus |
| 2019-04-02 | gnu: pigx-chipseq: Update to 0.0.40....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.40.
| Ricardo Wurmus |
| 2019-04-02 | gnu: python-scanpy: Add python-louvain to inputs....* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Sort
inputs and add python-louvain.
[arguments]: Do not delete test that depends on louvain.
| Ricardo Wurmus |
| 2019-03-31 | gnu: Fix descriptions to not use quotes....* gnu/packages/admin.scm (wpa-supplicant-minimal, mingetty, di),
* gnu/packages/audio.scm (fil-plugins),
* gnu/packages/base.scm (make-ld-wrapper, make-glibc-locales),
* gnu/packages/bioinformatics.scm (r-samtools),
* gnu/packages/chez.scm (chez-mit),
* gnu/packages/commencement.scm (make-gcc-toolchain),
* gnu/packages/compression.scm (fastjar),
* gnu/packages/cran.scm (r-maps, r-rcpp),
* gnu/packages/databases.scm (sparql-query),
* gnu/packages/dunst.scm (dunst),
* gnu/packages/ftp.scm (ncftp),
* gnu/packages/gl.scm (freeglut),
* gnu/packages/haskell-check.scm (ghc-tasty-golden),
* gnu/packages/haskell.scm (ghc-case-insensitive, ghc-text,
ghc-haskell-src, ghc-syb, ghc-deepseq-generics, ghc-network-uri,
ghc-rerebase, ghc-zlib),
* gnu/packages/image.scm (jbig2dec),
* gnu/packages/kde-frameworks.scm (kinit, karchive),
* gnu/packages/linux.scm (wireless-tools, perf, module-init-tools, kbd),
* gnu/packages/lirc.scm (lirc),
* gnu/packages/lisp.scm (uglify-js),
* gnu/packages/mate.scm (mate-netbook),
* gnu/packages/microcom.scm (microcom),
* gnu/packages/music.scm (bristol),
* gnu/packages/networking.scm (perl-geo-ip),
* gnu/packages/patchutils.scm (patches),
* gnu/packages/perl-check.scm (perl-test-more-utf8),
* gnu/packages/perl.scm (perl-log-report-optional, perl-file-which,
perl-io-tty, perl-log-any, perl-digest-sha1, perl-class-load,
perl-regexp-common, perl-module-pluggable, perl-class-modifier),
* gnu/packages/python-xyz.scm (python-backports-abc, python-natsort),
* gnu/packages/samba.scm (iniparser),
* gnu/packages/search.scm (mlocate),
* gnu/packages/spice.scm (spice),
* gnu/packages/statistics.scm (r-dt, r-lubridate, r-estimability,
r-commonmark, r-digest, r-viridislite, r-stringr),
* gnu/packages/tex.scm (texlive-latex-changebar),
* gnu/packages/version-control.scm (subversion),
* gnu/packages/w3m.scm (w3m),
* gnu/packages/web.scm (perl-http-parser,
perl-plack-middleware-reverseproxy),
* gnu/packages/xorg.scm (xkeyboard-config, mkfontdir, xcursor-theme,
mkfontscale, xinit, font-alias)[description]: Use @code instead of quotes.
| Efraim Flashner |
| 2019-03-29 | gnu: Add python-bbknn....* gnu/packages/bioinformatics.scm (python-bbknn): New variable.
| Ricardo Wurmus |
| 2019-03-27 | gnu: trim-galore: Add pigz....* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz.
[arguments]: Embed reference to pigz.
| Ricardo Wurmus |
| 2019-03-27 | gnu: trim-galore: Fix test for Python....* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace
"configure" phase to skip ill-advised test for Python.
| Ricardo Wurmus |
| 2019-03-27 | gnu: r-rhdf5lib: Update to 1.4.3....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.
| Ricardo Wurmus |
| 2019-03-27 | gnu: r-genomicfeatures: Update to 1.34.7....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.
| Ricardo Wurmus |
| 2019-03-26 | gnu: python-scanpy: Update to 1.4....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.
[source]: Fetch from git.
[arguments]: Disable broken tests.
[native-inputs]: Add python-pytest.
[home-page]: Use HTTPS.
| Ricardo Wurmus |
| 2019-03-26 | gnu: trim-galore: Update to 0.6.1....* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1.
[arguments]: Adjust patching.
| Ricardo Wurmus |
| 2019-03-26 | gnu: cutadapt: Update to 2.1....* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1.
[source]: Fetch from pypi.
[native-inputs]: Add python-setuptools-scm.
| Ricardo Wurmus |
| 2019-03-25 | gnu: r-gkmsvm: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here...
* gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.
| Ricardo Wurmus |
| 2019-03-25 | gnu: r-wgcna: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-wgcna): Move from here...
* gnu/packages/cran.scm (r-wgcna): ...to here.
| Ricardo Wurmus |
| 2019-03-25 | gnu: r-optparse: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-optparse): Move from here...
* gnu/packages/cran.scm (r-optparse): ...to here.
| Ricardo Wurmus |
| 2019-03-25 | gnu: r-bookdown: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-bookdown): Move from here...
* gnu/packages/cran.scm (r-bookdown): ...to here.
| Ricardo Wurmus |
| 2019-03-25 | gnu: r-sparql: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-sparql): Move from here...
* gnu/packages/cran.scm (r-sparql): ...to here.
| Ricardo Wurmus |
| 2019-03-24 | gnu: r-seqinr: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seqinr): Move from here...
* gnu/packages/cran.scm (r-seqinr): ...to here.
| Ricardo Wurmus |
| 2019-03-24 | gnu: r-acsnminer: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-acsnminer): Move from here...
* gnu/packages/cran.scm (r-acsnminer): ...to here.
| Ricardo Wurmus |
| 2019-03-24 | gnu: r-phangorn: Update to 2.5.3....* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.3.
| Ricardo Wurmus |
| 2019-03-24 | gnu: r-gqtlstats: Update to 1.14.1....* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.1.
| Ricardo Wurmus |
| 2019-03-24 | gnu: r-rbgl: Update to 1.58.2....* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.2.
| Ricardo Wurmus |
| 2019-03-22 | gnu: Add starlong....* gnu/packages/bioinformatics.scm (starlong): New variable.
| Ricardo Wurmus |
| 2019-03-21 | gnu: r-diversitree: Update to 0.9-11....* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
| Ricardo Wurmus |
| 2019-03-21 | gnu: r-maldiquant: Update to 1.19.2....* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
| Ricardo Wurmus |
| 2019-03-21 | gnu: r-diversitree: Fix typo....* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo
in package labels.
| Ricardo Wurmus |
| 2019-03-20 | gnu: r-annotationhub: Update to 2.14.5....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
| Ricardo Wurmus |
| 2019-03-20 | gnu: r-genomicfeatures: Update to 1.34.6....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
| Ricardo Wurmus |
| 2019-03-20 | gnu: r-variantannotation: Update to 1.28.13....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
| Ricardo Wurmus |
| 2019-03-20 | gnu: r-category: Update to 2.48.1....* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
| Ricardo Wurmus |
| 2019-03-20 | gnu: r-dexseq: Update to 1.28.3....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
| Ricardo Wurmus |
| 2019-03-20 | gnu: Add adapterremoval....* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
| Ricardo Wurmus |
| 2019-03-19 | gnu: nanopolish: Use python-wrapper....* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with
"python-wrapper" as scripts require "python" executable.
| Ricardo Wurmus |
| 2019-03-19 | gnu: nanopolish: Remove bundled library sources....* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove
bundled htslib sources.
| Ricardo Wurmus |
| 2019-03-18 | gnu: python-biom-format: Fix build....* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove
generated C files.
[arguments]: Disable second broken test.
| Ricardo Wurmus |
| 2019-03-18 | gnu: Add bbmap....* gnu/packages/bioinformatics.scm (bbmap): New variable.
| Ricardo Wurmus |
| 2019-03-18 | gnu: blasr: Add home page....Reported by Efraim Flashner <efraim@flashner.co.il> on IRC.
* gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
| Ricardo Wurmus |
| 2019-03-18 | gnu: Add arriba....* gnu/packages/bioinformatics.scm (arriba): New variable.
| Ricardo Wurmus |
| 2019-03-18 | gnu: Add blasr....* gnu/packages/bioinformatics.scm (blasr): New variable.
| Ricardo Wurmus |
| 2019-03-18 | gnu: Add blasr-libcpp....* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
| Ricardo Wurmus |
| 2019-03-18 | gnu: Add pbbam....* gnu/packages/bioinformatics.scm (pbbam): New variable.
| Ricardo Wurmus |
| 2019-03-15 | gnu: Add bwa-meth....* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
| Ricardo Wurmus |
| 2019-03-13 | gnu: Add python-velocyto....* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
| Ricardo Wurmus |
| 2019-03-13 | gnu: python-loompy: Update to 2.0.17....* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
| Ricardo Wurmus |
| 2019-03-13 | gnu: Add tetoolkit....* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
| Ricardo Wurmus |
| 2019-03-12 | gnu: r-qvalue: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-qvalue): Move from here...
* gnu/packages/bioconductor.scm (r-qvalue): ...to here.
| Ricardo Wurmus |
| 2019-03-08 | gnu: blast+: Update to 2.7.1....* gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1.
[inputs]: Add lmdb.
[source]: Remove obsolete patch.
* gnu/package/patches/blast+-fix-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2019-03-08 | gnu: r-mzr: Update to 2.16.2....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2.
[inputs]: Replace "boost" with "boost-for-mysql".
| Ricardo Wurmus |
