| Age | Commit message (Expand) | Author |
|---|
| 2018-04-10 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2018-04-06 | gnu: sambamba: Update to 0.6.7-10-g223fa20....* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
| Ricardo Wurmus |
| 2018-04-06 | gnu: htslib-for-sambamba: Fix build....* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
| Ricardo Wurmus |
| 2018-03-30 | gnu: Add delly....* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.
Signed-off-by: Leo Famulari <leo@famulari.name>
| Roel Janssen |
| 2018-03-30 | gnu: mash: Update to 2.0....* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
| Ben Woodcroft |
| 2018-03-30 | gnu: mafft: Update to 7.394....* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
| Ben Woodcroft |
| 2018-03-30 | gnu: diamond: Update to 0.9.19....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
| Ben Woodcroft |
| 2018-03-29 | Merge branch 'master' into core-updates | Marius Bakke |
| 2018-03-29 | gnu: r-mutationalpatterns: Update to 1.4.3....* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
[propagated-inputs]: Remove r-gridextra.
| Roel Janssen |
| 2018-03-29 | gnu: kaiju: Update to 1.6.2....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
[inputs]: Add zlib.
| Roel Janssen |
| 2018-03-27 | gnu: Use invoke and return #t from all builders....* gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm,
gnu/packages/avr.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm,
gnu/packages/certs.scm, gnu/packages/check.scm, gnu/packages/code.scm,
gnu/packages/commencement.scm, gnu/packages/dictionaries.scm,
gnu/packages/docbook.scm, gnu/packages/emacs.scm, gnu/packages/embedded.scm,
gnu/packages/fonts.scm, gnu/packages/games.scm, gnu/packages/gnome.scm,
gnu/packages/gnu-doc.scm, gnu/packages/guile.scm, gnu/packages/hurd.scm,
gnu/packages/javascript.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/mate.scm,
gnu/packages/pkg-config.scm, gnu/packages/qt.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/statistics.scm,
gnu/packages/syncthing.scm, gnu/packages/tex.scm, gnu/packages/web.scm,
gnu/packages/wine.scm, gnu/packages/xfce.scm: In the builders of packages
using 'trivial-build-system', use invoke where appropriate, raise exceptions
on errors, and otherwise return #t.
| Mark H Weaver |
| 2018-03-25 | gnu: r-annotate: Update to 1.56.2....* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
| Tobias Geerinckx-Rice |
| 2018-03-22 | gnu: r-bookdown: Do not propagate ghc-pandoc....This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.
* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
| Ricardo Wurmus |
| 2018-03-21 | gnu: pigx-chipseq: Update to 0.0.10....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
| Ricardo Wurmus |
| 2018-03-20 | gnu: pigx-chipseq: Update to 0.0.9....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
| Ricardo Wurmus |
| 2018-03-20 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2018-03-20 | gnu: pigx-bsseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
| Ricardo Wurmus |
| 2018-03-20 | gnu: pigx-rnaseq: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
| Ricardo Wurmus |
| 2018-03-20 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2018-03-19 | gnu: pigx-bsseq: Update to 0.0.7....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
| Ricardo Wurmus |
| 2018-03-19 | gnu: bismark: Fix references to gunzip....* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-scrnaseq: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx: Update to 0.0.2....* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
| Ricardo Wurmus |
| 2018-03-19 | gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1....* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-chipseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-scrnaseq: Use pandoc-1....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-bsseq: Use pandoc-1....* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-chipseq: Use pandoc-1....* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-rnaseq: Use pandoc-1....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
| Ricardo Wurmus |
| 2018-03-17 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2018-03-16 | gnu: Add pigx....* gnu/packages/bioinformatics.scm (pigx): New variable.
| Ricardo Wurmus |
| 2018-03-16 | gnu: pigx-rnaseq: Disable memory hungry test....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
| Ricardo Wurmus |
| 2018-03-16 | gnu: All snippets report errors using exceptions, else return #t....* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
| Mark H Weaver |
| 2018-03-16 | gnu: Add pigx-scrnaseq....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
| Ricardo Wurmus |
| 2018-03-16 | gnu: kentutils: Build with mariadb....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
| Ricardo Wurmus |
| 2018-03-16 | gnu: kentutils: Build with mariadb....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
| Ricardo Wurmus |
| 2018-03-15 | gnu: Add Diversitree....* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
| Leo Famulari |
| 2018-03-14 | Merge branch 'master' into core-updates | Ricardo Wurmus |
| 2018-03-11 | build-system/gnu: Add 'bootstrap' phase....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.
| Ludovic Courtès |
| 2018-03-11 | gnu: Add pigx-bsseq....* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
| Ricardo Wurmus |
| 2018-03-11 | gnu: Add pigx-chipseq....* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
| Ricardo Wurmus |
| 2018-03-09 | gnu: r-rhdf5lib: Make build reproducible....* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
| Ricardo Wurmus |
| 2018-03-08 | gnu: Add r-phangorn....* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
| Ricardo Wurmus |
| 2018-03-08 | gnu: r-ape: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
| Ricardo Wurmus |
| 2018-03-08 | gnu: r-dropbead: Update to 0-2.d746c6f....* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
| Ricardo Wurmus |
| 2018-03-07 | gnu: Add pigx-rnaseq....* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
| Ricardo Wurmus |
| 2018-03-06 | gnu: samtools: Update to 1.7....* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
| Ricardo Wurmus |
| 2018-03-06 | gnu: htslib: Update to 1.7....* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
| Ricardo Wurmus |
| 2018-03-06 | gnu: r-rhdf5: Make build reproducible....* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
| Ricardo Wurmus |
| 2018-03-04 | gnu: piranha: Declare a source file-name....* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
| Efraim Flashner |
