| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
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* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
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* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
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* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
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* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
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* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
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* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
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* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
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* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
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* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
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* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
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* gnu/packages/bioinformatics.scm (java-forester): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
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* gnu/packages/bioinformatics.scm (fastqc): New variable.
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* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
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* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
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* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
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* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
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* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
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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.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
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* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
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* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
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* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1.
[propagated-inputs]: Remove r-nmf; add r-metap.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
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* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
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* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7.
[propagated-inputs]: Add r-tinytex.
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