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2019-11-28Revert "gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and ↵Ricardo Wurmus
stumpwm to wm." This reverts commit abf43a67d5929bf279edce3e790ef1348dda32a5 as it broke "guix pull".
2019-11-28gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.Pierre Neidhardt
* gnu/local.mk: Include lisp-xyz.scm. * gnu/packages/lisp-xyz.scm: New file. * gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to javascript.scm and stumpwm to wm.scm. * gnu/packages/javascript.scm: Add uglify-js. * gnu/packages/wm.scm: Add stumpwm. * gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm. * gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm. * gnu/packages/web.scm: Find uglify-js in javascript.scm. * gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
2019-11-25gnu: libdivsufsort: Move to datastructures.scm.Efraim Flashner
* gnu/packages/bioinformatics.scm (libdivsufsort): Move to ... * gnu/packages/datastructures.scm: ... here.
2019-11-25gnu: bioperl-minimal: Don't use unstable tarball.Efraim Flashner
* gnu/packages/bioinformatics.scm (bioperl-minimal)[source]: Download using git-fetch.
2019-11-20gnu: ngless: Update to 1.0.1.Timothy Sample
* gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1. [arguments]: Add a 'create-Versions.hs' phase that patches the Makefile and invokes 'make' to generate a required file. [inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and 'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib', 'ghc-diagrams-svg', and 'ghc-tar-conduit'.
2019-11-14gnu: r-gprofiler: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
2019-11-10gnu: Add 'file-name' where appropriate.Efraim Flashner
* gnu/packages/admin.scm (detox, neofetch), gnu/packages/algebra.scm (python-fpylll), gnu/packages/bioinformatics.scm (tbsp, genrich), gnu/packages/crypto.scm (hpenc), gnu/packages/digest.scm (xxhash), gnu/packages/emacs-xyz.scm (emacs-tiny, emacs-ergoemacs-mode, emacs-make-it-so, emacs-poet-theme, emacs-deft, emacs-scribble-mode, emacs-helm-mu, emacs-unidecode, emacs-diff-hl, emacs-helm-exwm, emacs-gif-screencast, emacs-exec-path-from-shell), gnu/packages/engineering.scm (gpx), gnu/packages/freedesktop.scm (waylandpp), gnu/packages/golang.scm (go-github-com-sirupsen-logrus, go-github-com-shirou-gopsutil), gnu/packages/guile-xyz.scm (guile-studio, guile-picture-language, jupyter-guile-kernel), gnu/packages/image-viewers.scm (qview), gnu/packages/java-maths.scm (java-jblas), gnu/packages/llvm.scm (libclc), gnu/packages/logging.scm (spdlog), gnu/packages/ocaml.scm (ocaml-cstruct, ocaml-zarith), gnu/packages/terminals.scm (libtsm), gnu/packages/tigervnc.scm (tigervnc-client), gnu/packages/xdisorg.scm (xcalib, xbanish) [source]: Add file-name.
2019-10-20gnu: Remove more GCC < 7 workarounds.Marius Bakke
* gnu/packages/abiword.scm (abiword)[arguments]: Do not pass "-std=c++11" to the GCC command line. * gnu/packages/aidc.scm (zbar)[arguments]: Likewise. * gnu/packages/android.scm (android-libbase, android-libcutils, android-libziparchive, fastboot)[arguments]: Likewise. * gnu/packages/audio.scm (azr3, guitarix, suil)[arguments]: Likewise. * gnu/packages/bioinformatics.scm (bless)[arguments]: Likewise. * gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Likewise. * gnu/packages/code.scm (rtags)[arguments]: Likewise. * gnu/packages/coq.scm (coq-gappa)[arguments]: Likewise. * gnu/packages/emulators.scm (dolphin-emu)[arguments]: Likewise. * gnu/packages/engineering.scm (xyce-serial, xyce-parallel)[arguments]: Likewise. * gnu/packages/gnupg.scm (pinentry-qt)[arguments]: Likewise. * gnu/packages/gobby.scm (libnet6, obby)[arguments]: Likewise. * gnu/packages/graph.scm (python-faiss)[arguments]: Likewise. * gnu/packages/graphics.scm (povray)[arguments]: Likewise. * gnu/packages/image-processing.scm (opencv, itk-snap)[arguments]: Likewise. * gnu/packages/image.scm (freeimage)[arguments]: Likewise. * gnu/packages/kodi.scm (crossguid)[arguments]: Likewise. * gnu/packages/music.scm (amsynth, qmidiarp, qmidiroute, seq24)[arguments]: Likewise. * gnu/packages/pdf.scm (python-poppler-qt5)[arguments]: Likewise. * gnu/packages/sagemath.scm (lcalc)[arguments]: Likewise. * gnu/packages/video.scm (vlc, mlt, v4l-utils)[arguments]: Likewise.
2019-10-18gnu: r-rhdf5lib: Update to 1.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.3.
2019-10-18gnu: r-hdf5array: Update to 1.12.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.3.
2019-10-18gnu: r-gwascat: Update to 2.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.1.
2019-10-18gnu: r-ldblock: Update to 1.14.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.3.
2019-10-18gnu: r-ensembldb: Update to 2.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.1.
2019-10-18gnu: r-keggrest: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.1.
2019-10-18gnu: r-rhdf5: Update to 2.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.1.
2019-10-18gnu: r-rhtslib: Update to 1.16.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.3.
2019-10-18gnu: r-rsamtools: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.3.
2019-10-18gnu: bowtie1: Update to 1.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.2.3.
2019-10-14gnu: Add methyldackel.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel): New variable.
2019-10-14gnu: Add r-velocyto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-velocyto): New variable.
2019-10-07Merge branch 'master' into core-updatesLudovic Courtès
2019-10-06gnu: r-seurat: Update to 3.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1. [propagated-inputs]: Add r-httr.
2019-10-06gnu: r-rsamtools: Update to 2.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
2019-10-06gnu: r-biomart: Update to 2.40.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
2019-10-06Merge branch 'master' into core-updatesRicardo Wurmus
2019-10-03gnu: rcas-web: Fix build with RCAS > 1.3.x.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (rcas-web)[arguments]: Add ‘find-RCAS’ phase.
2019-10-01Merge branch 'master' into core-updatesLudovic Courtès
2019-09-28gnu: r-gviz: Update to 1.28.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.3.
2019-09-28gnu: r-mzr: Update to 2.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.1.
2019-09-28gnu: r-rhtslib: Update to 1.16.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.2.
2019-09-28gnu: r-rsamtools: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.1.
2019-09-28gnu: r-iranges: Update to 2.18.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.3.
2019-09-17Merge branch 'master' into core-updatesLudovic Courtès
2019-09-14gnu: r-delayedmatrixstats: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1.
2019-09-14gnu: r-rhdf5lib: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1.
2019-09-14gnu: r-rtracklayer: Update to 1.44.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4.
2019-09-14gnu: r-genomicranges: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
2019-09-14gnu: r-s4vectors: Update to 0.22.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
2019-09-08gnu: r-gprofiler: Update to 0.6.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.
2019-09-08gnu: r-annotationhub: Update to 2.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.
2019-09-08gnu: r-edger: Update to 3.26.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.
2019-09-06Merge branch 'master' into core-updatesMark H Weaver
2019-09-06gnu: Add samblaster.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samblaster): New variable.
2019-09-05gnu: libbigwig: Update to 0.4.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4.
2019-09-05gnu: python-pyfaidx: Remove python-setuptools as an input.Christopher Baines
As this is provided by the build system, and I'm assuming that it's not necessary to have it as a propagated input. * gnu/packages/bioinformatics.scm (python-pyfaidx)[propagated-inputs]: Remove python-setuptools.
2019-09-05gnu: umi-tools: Remove python-setuptools as an input.Christopher Baines
As this is provided by the build system. * gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove python-setuptools.
2019-09-05gnu: bwa-meth: Capture one more reference to "bwa".Ricardo Wurmus
Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de> * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of "bwa index" to retain reference to "bwa" package.
2019-09-02gnu: r-ldblock: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.2. [propagated-inputs]: Remove r-erma; add r-ensdb-hsapiens-v75, r-ensembldb, and r-httr.
2019-09-02gnu: r-seurat: Update to 3.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0. [propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot.
2019-09-02gnu: r-rtracklayer: Update to 1.44.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3.
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