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* Merge branch 'master' into core-updatesRicardo Wurmus2018-03-14
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| * gnu: Add pigx-bsseq.Ricardo Wurmus2018-03-11
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
| * gnu: Add pigx-chipseq.Ricardo Wurmus2018-03-11
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
| * gnu: r-rhdf5lib: Make build reproducible.Ricardo Wurmus2018-03-09
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp and host system kernel version.
| * gnu: Add r-phangorn.Ricardo Wurmus2018-03-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-phangorn): New variable.
| * gnu: r-ape: Move to (gnu packages cran).Ricardo Wurmus2018-03-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-ape): Move from here... * gnu/packages/cran.scm (r-ape): ...to here.
| * gnu: r-dropbead: Update to 0-2.d746c6f.Ricardo Wurmus2018-03-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
| * gnu: Add pigx-rnaseq.Ricardo Wurmus2018-03-07
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
| * gnu: samtools: Update to 1.7.Ricardo Wurmus2018-03-06
| | | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
| * gnu: htslib: Update to 1.7.Ricardo Wurmus2018-03-06
| | | | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.7. [arguments]: Remove field.
| * gnu: r-rhdf5: Make build reproducible.Ricardo Wurmus2018-03-06
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and host system information from settings file.
| * gnu: piranha: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source file-name.
| * gnu: libdivsufsort: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a source file-name.
| * gnu: seek: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (seek)[source]: Declare a source file-name.
| * gnu: r-dropbead: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source file-name.
| * gnu: Add dropseq-tools.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
| * gnu: Add java-picard-2.10.3.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
| * gnu: Add java-htsjdk-2.10.1.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
| * gnu: Add java-htsjdk-latest.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
| * gnu: Add java-biojava-alignment-4.0.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
| * gnu: Add java-biojava-phylo-4.0.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
| * gnu: Add java-biojava-core-4.0.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
| * gnu: Add java-biojava-alignment.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
| * gnu: Add java-biojava-phylo.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
| * gnu: Add java-forester-1.005.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
| * gnu: Add java-forester.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-forester): New variable.
| * gnu: Add java-biojava-core.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
| * gnu: Add fastqc.Ricardo Wurmus2018-03-03
| | | | | | | | * gnu/packages/bioinformatics.scm (fastqc): New variable.
| * gnu: cutadapt: Update to 1.16.Ricardo Wurmus2018-03-02
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16. [source]: Fetch via git. [arguments]: Remove. [native-inputs]: Replace python-nose with python-pytest.
| * gnu: r-scran: Update to 1.6.8.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
| * gnu: r-wgcna: Update to 1.63.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
| * gnu: r-topgo: Update to 2.30.1.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
| * gnu: r-genomicranges: Update to 1.30.3.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
| * gnu: r-limma: Update to 3.34.9.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
| * gnu: r-edger: Update to 3.20.9.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
| * gnu: r-shortread: Update to 1.36.1.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
| * gnu: r-dexseq: Update to 1.24.3.Ricardo Wurmus2018-03-01
| | | | | | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
* | build-system/gnu: Add 'bootstrap' phase.Ludovic Courtès2018-03-11
|/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This factorizes what has become a widespread idiom. * guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable. (bootstrap): New procedure. (%standard-phases): Add it after 'unpack'. * guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap. * guix/build/asdf-build-system.scm (%standard-phases/source) (%standard-phases): Likewise. * guix/build/cargo-build-system.scm (%standard-phases): Likewise. * guix/build/cmake-build-system.scm (%standard-phases): Likewise. * guix/build/dub-build-system.scm (%standard-phases): Likewise. * guix/build/emacs-build-system.scm (%standard-phases): Likewise. * guix/build/font-build-system.scm (%standard-phases): Likewise. * guix/build/go-build-system.scm (%standard-phases): Likewise. * guix/build/haskell-build-system.scm (%standard-phases): Likewise. * guix/build/minify-build-system.scm (%standard-phases): Likewise. * guix/build/ocaml-build-system.scm (%standard-phases): Likewise. * guix/build/perl-build-system.scm (%standard-phases): Likewise. * guix/build/python-build-system.scm (%standard-phases): Likewise. * guix/build/r-build-system.scm (%standard-phases): Likewise. * guix/build/ruby-build-system.scm (%standard-phases): Likewise. * guix/build/scons-build-system.scm (%standard-phases): Likewise. * guix/build/texlive-build-system.scm (%standard-phases): Likewise. * guix/build/waf-build-system.scm (%standard-phases): Likewise. * gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap. (soundtouch, cuetools, bluez-alsa): Remove 'arguments'. (cava)[arguments]: Replace 'bootstrap. * gnu/packages/backup.scm (rdup): Remove 'bootstrap. * gnu/packages/bioinformatics.scm (seek)[arguments]: Replace 'bootstrap. * gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove 'arguments'. * gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'. * gnu/packages/crypto.scm (libb2): Remove #:phases. * gnu/packages/databases.scm (guile-wiredtiger): Likewise. * gnu/packages/debug.scm (stress-make): Remove 'bootstrap'. * gnu/packages/documentation.scm (asciidoc): Likewise. * gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'. * gnu/packages/ftp.scm (weex): Remove 'arguments'. * gnu/packages/game-development.scm (ois): Remove 'arguments'. * gnu/packages/games.scm (pioneer): Remove 'bootstrap. * gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap. (arc-theme): Remove 'arguments'. (faba-icon-theme): Remove 'bootstrap. (arc-icon-theme): Remove 'arguments'. * gnu/packages/gnunet.scm (guile-gnunet): Likewise. * gnu/packages/gtk.scm (guile-rsvg): Likewise. * gnu/packages/guile.scm (mcron2): Remove 'bootstrap. (guile-bash): Remove #:phases. (guile-git): Remove 'bootstrap. (guile-syntax-highlight): Remove 'arguments'. (guile-sjson): Likewise. * gnu/packages/java.scm (classpath-devel): Remove 'bootstrap. * gnu/packages/kodi.scm (libdvdnav/kodi) (libdvdread/kodi, libdvdcss/kodi): Likewise. * gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'. * gnu/packages/libusb.scm (hidapi): Likewise. * gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to 'patch-stuff'; move it before 'bootstrap', without autoreconf invocation. (eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh' invocation; move it before 'bootstrap. (gpm): Replace 'bootstrap'. (f2fs-tools): Remove 'arguments'. (rng-tools): Remove #:phases. * gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to 'copy-intltool-makefile'; remove "autoreconf" invocation and move before 'bootstrap'. (libmesode): Remove 'arguments'. (libstrophe): Likewise. * gnu/packages/microcom.scm (microcom): Likewise. * gnu/packages/networking.scm (libnet): Remove 'bootstrap. * gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'. * gnu/packages/package-management.scm (guix): Replace 'bootstrap. * gnu/packages/sawfish.scm (librep): Remove 'arguments'. * gnu/packages/version-control.scm (findnewest): Likewise. * gnu/packages/video.scm (liba52, handbrake, motion): Replace 'bootstrap. * gnu/packages/web.scm (fcgiwrap): Remove #:phases. (tidy): Replace 'bootstrap. (gumbo-parser): Remove #:phases. * gnu/packages/wget.scm (wget2): Replace 'bootstrap. * gnu/packages/wm.scm (i3lock-color): Remove #:phases. * gnu/packages/xdisorg.scm (xclip): Likewise. * gnu/packages/xml.scm (libxls): Replace 'bootstrap'. * gnu/packages/xorg.scm (xf86-video-freedreno) (xf86-video-intel): Remove #:phases. * gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
* gnu: r-qtl: Update to 1.42-8.Ricardo Wurmus2018-02-22
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
* gnu: r-delayedmatrixstats: Update to 1.0.3.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
* gnu: r-scater: Update to 1.6.3.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
* gnu: r-gviz: Update to 1.22.3.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
* gnu: r-gprofiler: Update to 0.6.4.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
* gnu: r-ensembldb: Update to 2.2.2.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
* gnu: r-seurat: Update to 2.2.1.Ricardo Wurmus2018-02-19
| | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1. [propagated-inputs]: Remove r-nmf; add r-metap.
* gnu: r-qtl: Update to 1.42-7.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
* gnu: r-genomicranges: Update to 1.30.2.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
* gnu: r-getopt: Update to 1.20.2.Ricardo Wurmus2018-02-19
| | | | * gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
* gnu: r-bookdown: Update to 0.7.Ricardo Wurmus2018-02-19
| | | | | * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7. [propagated-inputs]: Add r-tinytex.
* Merge branch 'master' into core-updatesRicardo Wurmus2018-02-18
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