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2018-03-20Merge branch 'master' into core-updatesMark H Weaver
2018-03-20gnu: pigx-bsseq: Update to 0.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
2018-03-20gnu: pigx-rnaseq: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3. [inputs]: Add gzip.
2018-03-20Merge branch 'master' into core-updatesMark H Weaver
2018-03-19gnu: pigx-bsseq: Update to 0.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep.
2018-03-19gnu: bismark: Fix references to gunzip.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip.
2018-03-19gnu: pigx-scrnaseq: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl.
2018-03-19gnu: pigx: Update to 0.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
2018-03-19gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: pigx-chipseq: Update to 0.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests.
2018-03-19gnu: pigx-scrnaseq: Use pandoc-1.Ricardo Wurmus
* 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.
2018-03-19gnu: pigx-bsseq: Use pandoc-1.Ricardo Wurmus
* 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.
2018-03-19gnu: pigx-chipseq: Use pandoc-1.Ricardo Wurmus
* 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.
2018-03-19gnu: pigx-rnaseq: Use pandoc-1.Ricardo Wurmus
* 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.
2018-03-17Merge branch 'master' into core-updatesMark H Weaver
2018-03-16gnu: Add pigx.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx): New variable.
2018-03-16gnu: pigx-rnaseq: Disable memory hungry test.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to disable a memory hungry test.
2018-03-16gnu: All snippets report errors using exceptions, else return #t.Mark H Weaver
* 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.
2018-03-16gnu: Add pigx-scrnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
2018-03-16gnu: kentutils: Build with mariadb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with mariadb.
2018-03-16gnu: kentutils: Build with mariadb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with mariadb.
2018-03-15gnu: Add Diversitree.Leo Famulari
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
2018-03-14Merge branch 'master' into core-updatesRicardo Wurmus
2018-03-11build-system/gnu: Add 'bootstrap' phase.Ludovic Courtès
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.
2018-03-11gnu: Add pigx-bsseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
2018-03-11gnu: Add pigx-chipseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
2018-03-09gnu: r-rhdf5lib: Make build reproducible.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp and host system kernel version.
2018-03-08gnu: Add r-phangorn.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
2018-03-08gnu: r-ape: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ape): Move from here... * gnu/packages/cran.scm (r-ape): ...to here.
2018-03-08gnu: r-dropbead: Update to 0-2.d746c6f.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
2018-03-07gnu: Add pigx-rnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
2018-03-06gnu: samtools: Update to 1.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
2018-03-06gnu: htslib: Update to 1.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7. [arguments]: Remove field.
2018-03-06gnu: r-rhdf5: Make build reproducible.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and host system information from settings file.
2018-03-04gnu: piranha: Declare a source file-name.Efraim Flashner
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source file-name.
2018-03-04gnu: libdivsufsort: Declare a source file-name.Efraim Flashner
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a source file-name.
2018-03-04gnu: seek: Declare a source file-name.Efraim Flashner
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source file-name.
2018-03-04gnu: r-dropbead: Declare a source file-name.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source file-name.
2018-03-03gnu: Add dropseq-tools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
2018-03-03gnu: Add java-picard-2.10.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
2018-03-03gnu: Add java-htsjdk-2.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
2018-03-03gnu: Add java-htsjdk-latest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
2018-03-03gnu: Add java-biojava-alignment-4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
2018-03-03gnu: Add java-biojava-phylo-4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
2018-03-03gnu: Add java-biojava-core-4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
2018-03-03gnu: Add java-biojava-alignment.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
2018-03-03gnu: Add java-biojava-phylo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
2018-03-03gnu: Add java-forester-1.005.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
2018-03-03gnu: Add java-forester.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-forester): New variable.
2018-03-03gnu: Add java-biojava-core.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
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