summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
Commit message (Collapse)AuthorAge
* Merge branch 'master' into stagingMarius Bakke2019-11-28
|\
| * gnu: libdivsufsort: Move to datastructures.scm.Efraim Flashner2019-11-25
| | | | | | | | | | * gnu/packages/bioinformatics.scm (libdivsufsort): Move to ... * gnu/packages/datastructures.scm: ... here.
| * gnu: bioperl-minimal: Don't use unstable tarball.Efraim Flashner2019-11-25
| | | | | | | | | | * gnu/packages/bioinformatics.scm (bioperl-minimal)[source]: Download using git-fetch.
* | Merge branch 'master' into stagingMarius Bakke2019-11-21
|\|
| * gnu: ngless: Update to 1.0.1.Timothy Sample2019-11-20
| | | | | | | | | | | | | | | | | | * 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'.
* | Merge branch 'master' into stagingMarius Bakke2019-11-15
|\|
| * gnu: r-gprofiler: Update to 0.7.0.Ricardo Wurmus2019-11-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
| * gnu: Add 'file-name' where appropriate.Efraim Flashner2019-11-10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | Merge branch 'master' into stagingMarius Bakke2019-10-21
|\|
| * gnu: Remove more GCC < 7 workarounds.Marius Bakke2019-10-20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * gnu: r-rhdf5lib: Update to 1.6.3.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.3.
| * gnu: r-hdf5array: Update to 1.12.3.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.3.
| * gnu: r-gwascat: Update to 2.16.1.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.1.
| * gnu: r-ldblock: Update to 1.14.3.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.3.
| * gnu: r-ensembldb: Update to 2.8.1.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.1.
| * gnu: r-keggrest: Update to 1.24.1.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.1.
| * gnu: r-rhdf5: Update to 2.28.1.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.1.
| * gnu: r-rhtslib: Update to 1.16.3.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.3.
| * gnu: r-rsamtools: Update to 2.0.3.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.3.
| * gnu: bowtie1: Update to 1.2.3.Ricardo Wurmus2019-10-18
| | | | | | | | * gnu/packages/bioinformatics.scm (bowtie1): Update to 1.2.3.
* | Merge branch 'master' into stagingMarius Bakke2019-10-18
|\|
| * gnu: Add methyldackel.Ricardo Wurmus2019-10-14
| | | | | | | | * gnu/packages/bioinformatics.scm (methyldackel): New variable.
| * gnu: Add r-velocyto.Ricardo Wurmus2019-10-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-velocyto): New variable.
* | gnu: mariadb: Split into out, lib and dev.Julien Lepiller2019-10-12
|/ | | | | | | | | | | * gnu/packages/databases.scm (mariadb): Split into out, lib and dev. (perl-dbd-mysql, python-mysqlclient): Adjust dependencies. * gnu/packages/bioinformatics.scm (kentutils): Adjust dependencies. * gnu/packages/cran.scm (r-rmysql): Adjust dependencies. * gnu/packages/emacs-xyz.scm (emacs-emacsql): Adjust dependencies. * gnu/packages/kodi.scm (kodi): Adjust dependencies. * gnu/packages/qt.scm (qt, qtbase): Adjust dependencies. * gnu/packages/ruby.scm (ruby-mysql2): Adjust dependencies.
* Merge branch 'master' into core-updatesLudovic Courtès2019-10-07
|\
| * gnu: r-seurat: Update to 3.1.1.Ricardo Wurmus2019-10-06
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1. [propagated-inputs]: Add r-httr.
| * gnu: r-rsamtools: Update to 2.0.2.Ricardo Wurmus2019-10-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
| * gnu: r-biomart: Update to 2.40.5.Ricardo Wurmus2019-10-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
* | Merge branch 'master' into core-updatesRicardo Wurmus2019-10-06
|\|
| * gnu: rcas-web: Fix build with RCAS > 1.3.x.Tobias Geerinckx-Rice2019-10-03
| | | | | | | | * gnu/packages/bioinformatics.scm (rcas-web)[arguments]: Add ‘find-RCAS’ phase.
* | Merge branch 'master' into core-updatesLudovic Courtès2019-10-01
|\|
| * gnu: r-gviz: Update to 1.28.3.Ricardo Wurmus2019-09-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.3.
| * gnu: r-mzr: Update to 2.18.1.Ricardo Wurmus2019-09-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.1.
| * gnu: r-rhtslib: Update to 1.16.2.Ricardo Wurmus2019-09-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.2.
| * gnu: r-rsamtools: Update to 2.0.1.Ricardo Wurmus2019-09-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.1.
| * gnu: r-iranges: Update to 2.18.3.Ricardo Wurmus2019-09-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.3.
* | Merge branch 'master' into core-updatesLudovic Courtès2019-09-17
|\|
| * gnu: r-delayedmatrixstats: Update to 1.6.1.Ricardo Wurmus2019-09-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1.
| * gnu: r-rhdf5lib: Update to 1.6.1.Ricardo Wurmus2019-09-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1.
| * gnu: r-rtracklayer: Update to 1.44.4.Ricardo Wurmus2019-09-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4.
| * gnu: r-genomicranges: Update to 1.36.1.Ricardo Wurmus2019-09-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
| * gnu: r-s4vectors: Update to 0.22.1.Ricardo Wurmus2019-09-14
| | | | | | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
| * gnu: r-gprofiler: Update to 0.6.8.Ricardo Wurmus2019-09-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.
| * gnu: r-annotationhub: Update to 2.16.1.Ricardo Wurmus2019-09-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.
| * gnu: r-edger: Update to 3.26.8.Ricardo Wurmus2019-09-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.
* | Merge branch 'master' into core-updatesMark H Weaver2019-09-06
|\|
| * gnu: Add samblaster.Ricardo Wurmus2019-09-06
| | | | | | | | * gnu/packages/bioinformatics.scm (samblaster): New variable.
| * gnu: libbigwig: Update to 0.4.4.Ricardo Wurmus2019-09-05
| | | | | | | | * gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4.
| * gnu: python-pyfaidx: Remove python-setuptools as an input.Christopher Baines2019-09-05
| | | | | | | | | | | | | | | | 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.
| * gnu: umi-tools: Remove python-setuptools as an input.Christopher Baines2019-09-05
| | | | | | | | | | | | | | As this is provided by the build system. * gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove python-setuptools.
generated by cgit v1.2.3 (git 2.25.4) at 2024-10-19 19:14:07 +0000