| Age | Commit message (Expand) | Author |
|---|
| 2017-10-07 | gnu: vsearch: Update to 2.5.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.0.
| Ben Woodcroft |
| 2017-09-23 | gnu: proteinortho: Update to 5.16b....* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
| Ben Woodcroft |
| 2017-09-22 | gnu: Use xxd instead of vim....* gnu/packages/audio.scm (faust-2)[native-inputs]: Replace vim with xxd.
* gnu/packages/avr.scm (microscheme)[native-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (star)[native-inputs]: Likewise.
* gnu/packages/disk.scm (dosfstools)[native-inputs]: Likewise.
* gnu/packages/package-management.scm (diffoscope)[inputs]: Likewise.
| Ricardo Wurmus |
| 2017-09-18 | gnu: r-rcas: Add missing inputs....* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Add r-pbapply.
| Ricardo Wurmus |
| 2017-09-18 | gnu: r-rcas: Update to 1.3.4....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.4.
| Ricardo Wurmus |
| 2017-09-10 | gnu: Fix build failures caused by commit...d10092b849153dc27cfed0a9601fde6c7bdec918.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase
order.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
| Kei Kebreau |
| 2017-09-05 | gnu: Add r-sparql....* gnu/packages/bioinformatics.scm (r-sparql): New variable.
| Roel Janssen |
| 2017-09-04 | gnu: Put autoconf-related phases immediately after the 'unpack phase....* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
| Kei Kebreau |
| 2017-09-01 | gnu: r-genomicalignments: Update to 1.12.2....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-vegan: Update to 2.4-4....* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4.
[native-inputs]: Remove r-knitr.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-maldiquant: Update to 1.16.4....* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-bookdown: Update to 0.5....* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-rcas: Correct license....* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
| Ricardo Wurmus |
| 2017-09-01 | gnu: r-rcas: Update to 1.3.3....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
| Ricardo Wurmus |
| 2017-09-01 | gnu: vsearch: Update to 2.4.4....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
| Ben Woodcroft |
| 2017-09-01 | gnu: metabat: Update to 2.12.1....* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it. Use url-fetch.
| Ben Woodcroft |
| 2017-08-31 | gnu: bioinformatics: Work around more "dotless @INC" build failures....* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
| Ben Woodcroft |
| 2017-08-31 | gnu: metabat: Update to 2.11.3....* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch. Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ben Woodcroft |
| 2017-08-30 | gnu: multiqc: Update to 1.2....* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2.
[source]: Remove patches.
[arguments]: Remove to enable tests.
[propagated-inputs]: Add python-spectra, python-requests, python-markdown,
python-lzstring.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2017-08-21 | Merge branch 'master' into core-updates | Marius Bakke |
| 2017-08-20 | gnu: Add r-annotationfilter....* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-methylkit....* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-qvalue....* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-fastseg....* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-annotationhub....* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
| Ricardo Wurmus |
| 2017-08-17 | gnu: Add r-interactivedisplaybase....* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
| Ricardo Wurmus |
| 2017-08-16 | gnu: r-mzr: Fix building on aarch64 and armhf....* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
| Efraim Flashner |
| 2017-08-15 | gnu: diamond: Update to 0.9.10....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
| Ben Woodcroft |
| 2017-08-15 | gnu: bcftools: Fix building on aarch64....* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: New file.
* gnu/packages/bioinformatics.scm (bcftools)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
| Efraim Flashner |
| 2017-08-15 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2017-08-14 | gnu: Add bismark....* gnu/packages/bioinformatics.scm (bismark): New variable.
| Ricardo Wurmus |
| 2017-08-14 | gnu: Add r-dexseq....* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
| Ricardo Wurmus |
| 2017-08-09 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2017-08-09 | gnu: r-wgcna: Update to 1.61....* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
| Ricardo Wurmus |
| 2017-08-09 | gnu: Add reference to (gnu packages graph)....This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3.
| Ricardo Wurmus |
| 2017-08-07 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2017-08-07 | gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash....* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place. It changed back.
This reverts commit fd4085793818ab2aea28dfeeb2728f6f02416c4c.
| Tobias Geerinckx-Rice |
| 2017-08-06 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2017-08-05 | gnu: perl: Work around more "dotless @INC" build issues....* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path'
phase.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment
'configure' phase to set PERL5LIB.
* gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
| Ludovic Courtès |
| 2017-08-03 | gnu: bioinformatics.scm: Use (gnu packages cran) module....This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249.
* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
| Efraim Flashner |
| 2017-08-03 | gnu: r-seqminer: Update to 6.0....* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
| Ricardo Wurmus |
| 2017-08-03 | gnu: r-wgcna: Update to 1.60....* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
| Ricardo Wurmus |
| 2017-08-03 | gnu: r-qtl: Update to 1.41-6....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
| Ricardo Wurmus |
| 2017-08-03 | gnu: r-seqinr: Update to 3.4-5....* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
| Ricardo Wurmus |
| 2017-08-03 | gnu: r-optparse: Update to 1.4.4....* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
| Ricardo Wurmus |
| 2017-08-03 | gnu: r-bookdown: Update to 0.4....* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
| Ricardo Wurmus |
| 2017-08-03 | gnu: htseq: Use PyPI URI....This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf.
* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
| Ben Woodcroft |
| 2017-08-03 | gnu: htseq: Update to 0.9.1....* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package. Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
| Ben Woodcroft |
| 2017-08-02 | gnu: r-deseq2: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
| Roel Janssen |
| 2017-08-02 | gnu: r-annotationforge: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
| Roel Janssen |
