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* gnu: Fix build failures caused by commitKei Kebreau2017-09-10
| | | | | | | | d10092b849153dc27cfed0a9601fde6c7bdec918. * gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase order. * gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
* gnu: Add r-sparql.Roel Janssen2017-09-05
| | | | * gnu/packages/bioinformatics.scm (r-sparql): New variable.
* gnu: Put autoconf-related phases immediately after the 'unpack phase.Kei Kebreau2017-09-04
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: r-genomicalignments: Update to 1.12.2.Ricardo Wurmus2017-09-01
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
* gnu: r-vegan: Update to 2.4-4.Ricardo Wurmus2017-09-01
| | | | | * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4. [native-inputs]: Remove r-knitr.
* gnu: r-maldiquant: Update to 1.16.4.Ricardo Wurmus2017-09-01
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
* gnu: r-bookdown: Update to 0.5.Ricardo Wurmus2017-09-01
| | | | * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
* gnu: r-rcas: Correct license.Ricardo Wurmus2017-09-01
| | | | * gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
* gnu: r-rcas: Update to 1.3.3.Ricardo Wurmus2017-09-01
| | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
* gnu: vsearch: Update to 2.4.4.Ben Woodcroft2017-09-01
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
* gnu: metabat: Update to 2.12.1.Ben Woodcroft2017-09-01
| | | | | | | * 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.
* gnu: bioinformatics: Work around more "dotless @INC" build failures.Ben Woodcroft2017-08-31
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add 'set-perl-search-path' phase.
* gnu: metabat: Update to 2.11.3.Ben Woodcroft2017-08-31
| | | | | | | * 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.
* gnu: multiqc: Update to 1.2.Ricardo Wurmus2017-08-30
| | | | | | | | | | * 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.
* Merge branch 'master' into core-updatesMarius Bakke2017-08-21
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| * gnu: Add r-annotationfilter.Ricardo Wurmus2017-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
| * gnu: Add r-methylkit.Ricardo Wurmus2017-08-17
| | | | | | | | * gnu/packages/bioinformatics.scm (r-methylkit): New variable.
| * gnu: Add r-qvalue.Ricardo Wurmus2017-08-17
| | | | | | | | * gnu/packages/bioinformatics.scm (r-qvalue): New variable.
| * gnu: Add r-fastseg.Ricardo Wurmus2017-08-17
| | | | | | | | * gnu/packages/bioinformatics.scm (r-fastseg): New variable.
| * gnu: Add r-annotationhub.Ricardo Wurmus2017-08-17
| | | | | | | | * gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
| * gnu: Add r-interactivedisplaybase.Ricardo Wurmus2017-08-17
| | | | | | | | * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
| * gnu: r-mzr: Fix building on aarch64 and armhf.Efraim Flashner2017-08-16
| | | | | | | | * gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
| * gnu: diamond: Update to 0.9.10.Ben Woodcroft2017-08-15
| | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
| * gnu: bcftools: Fix building on aarch64.Efraim Flashner2017-08-15
| | | | | | | | | | | | * 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.
* | Merge branch 'master' into core-updatesMark H Weaver2017-08-15
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| * gnu: Add bismark.Ricardo Wurmus2017-08-14
| | | | | | | | * gnu/packages/bioinformatics.scm (bismark): New variable.
| * gnu: Add r-dexseq.Ricardo Wurmus2017-08-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-dexseq): New variable.
* | Merge branch 'master' into core-updatesMark H Weaver2017-08-09
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| * gnu: r-wgcna: Update to 1.61.Ricardo Wurmus2017-08-09
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61. [propagated-inputs]: Add r-rcpp, r-robust, r-survival.
| * gnu: Add reference to (gnu packages graph).Ricardo Wurmus2017-08-09
| | | | | | | | This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3.
* | Merge branch 'master' into core-updatesMark H Weaver2017-08-07
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| * gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.Tobias Geerinckx-Rice2017-08-07
| | | | | | | | | | | | | | * 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.
* | Merge branch 'master' into core-updatesMark H Weaver2017-08-06
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| * gnu: bioinformatics.scm: Use (gnu packages cran) module.Efraim Flashner2017-08-03
| | | | | | | | | | | | This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
| * gnu: r-seqminer: Update to 6.0.Ricardo Wurmus2017-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
| * gnu: r-wgcna: Update to 1.60.Ricardo Wurmus2017-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
| * gnu: r-qtl: Update to 1.41-6.Ricardo Wurmus2017-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
| * gnu: r-seqinr: Update to 3.4-5.Ricardo Wurmus2017-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
| * gnu: r-optparse: Update to 1.4.4.Ricardo Wurmus2017-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
| * gnu: r-bookdown: Update to 0.4.Ricardo Wurmus2017-08-03
| | | | | | | | * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
| * gnu: htseq: Use PyPI URI.Ben Woodcroft2017-08-03
| | | | | | | | | | | | This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
| * gnu: htseq: Update to 0.9.1.Ben Woodcroft2017-08-03
| | | | | | | | | | | | | | | | | | | | * 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.
| * gnu: r-deseq2: Update to 1.16.1.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
| * gnu: r-annotationforge: Update to 1.18.1.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
| * gnu: r-category: Update to 2.42.1.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
| * gnu: r-biocstyle: Update to 2.4.1.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
| * gnu: r-dnacopy: Update to 1.50.1.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
| * gnu: r-iranges: Update to 2.10.2.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
| * gnu: r-genomeinfodb: Update to 1.12.2.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
| * gnu: r-variantannotation: Update to 1.22.3.Roel Janssen2017-08-02
| | | | | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
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