summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
Commit message (Collapse)AuthorAge
* Merge remote-tracking branch 'origin/master' into stagingEfraim Flashner2020-09-05
|\
| * gnu: delly: Update to 0.8.3.Efraim Flashner2020-08-30
| | | | | | | | | | * gnu/packages/bioinformatics.scm (delly): Update to 0.8.3. [inputs]: Order alphabetically.
| * gnu: vcflib: Install pkgconfig file.Efraim Flashner2020-08-27
| | | | | | | | | | * gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom 'install phase to add vcflib.pc.
| * gnu: vcflib: Use shared libraries.Efraim Flashner2020-08-27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add snippet to adjust files for new locations. [inputs]: Add fastahack, smithwaterman, tabixpp, xz. [native-inputs]: Add pkg-config. Remove the package-source of fastahack, fsom, smithwaterman, tabixpp. [arguments]: Remove make-flags. Add custom phase to add the output lib directory to the rpath. Adjust custom 'unpack-submodule-sources for the change in native-inputs. Adjust custom 'install phase to also install libraries and headers. * gnu/packages/patches/vcflib-use-shared-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
| * gnu: fastahack: Install pkgconfig file.Efraim Flashner2020-08-27
| | | | | | | | | | * gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom 'install phase to add fastahack.pc.
| * gnu: fastahack: Build and install shared library and headers.Efraim Flashner2020-08-27
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to build PIE objects. Add custom phase to build dynamic library. Adjust custom 'install phase to install shared library and headers.
| * gnu: smithwaterman: Install pkgconfig file.Efraim Flashner2020-08-27
| | | | | | | | | | * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust custom 'install phase to add smithwaterman.pc file.
| * gnu: smithwaterman: Build and install shared library and headers.Efraim Flashner2020-08-27
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom phase to build PIE objects. Add custom 'build-dynamic phase to build dynamic library. Adjust custom 'install phase to install shared library and headers.
| * gnu: tabixpp: Install pkgconfig file.Efraim Flashner2020-08-27
| | | | | | | | | | * gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom 'install phase to add tabixpp.pc file.
| * gnu: tabixpp: Build and install shared library and headers.Efraim Flashner2020-08-27
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom 'build phase to build shared library. Adjust custom 'install phase to install libraries and header.
| * gnu: r-complexheatmap: Update to 2.4.3.Ricardo Wurmus2020-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
| * gnu: r-gage: Update to 2.38.3.Ricardo Wurmus2020-08-20
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3. [propagated-inputs]: Add r-go-db.
| * gnu: r-annotationhub: Update to 2.20.2.Ricardo Wurmus2020-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
| * gnu: r-delayedarray: Update to 0.14.1.Ricardo Wurmus2020-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
| * gnu: r-annotationdbi: Update to 1.50.3.Ricardo Wurmus2020-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
| * gnu: r-biocviews: Update to 1.56.2.Ricardo Wurmus2020-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
| * gnu: pigx-chipseq: Update to 0.0.43.Ricardo Wurmus2020-08-19
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
| * gnu: bowtie1: Add missing Python input.Ricardo Wurmus2020-08-18
| | | | | | | | | | | | Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de> * gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
| * gnu: pigx-bsseq: Update to 0.1.2.Ricardo Wurmus2020-08-16
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2. [inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
| * gnu: pigx-scrnaseq: Use statically linked Pandoc.Ricardo Wurmus2020-08-16
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| * gnu: pigx-bsseq: Use statically linked Pandoc.Ricardo Wurmus2020-08-16
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| * gnu: pigx-chipseq: Use statically linked Pandoc.Ricardo Wurmus2020-08-16
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| * gnu: pigx-rnaseq: Use statically linked Pandoc.Ricardo Wurmus2020-08-16
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
| * gnu: r-rcas: Use pandoc instead of ghc-pandoc.Ricardo Wurmus2020-08-16
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Replace ghc-pandoc with pandoc.
| * gnu: hisat2: Use pandoc instead of ghc-pandoc.Ricardo Wurmus2020-08-15
| | | | | | | | | | * gnu/packages/bioinformatics.scm (hisat2)[native-inputs]: Replace ghc-pandoc with pandoc.
| * gnu: tophat: Hide default GCC.Ricardo Wurmus2020-08-12
| | | | | | | | | | * gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase "hide-default-gcc".
| * gnu: r-seurat: Update to 3.2.0.Ricardo Wurmus2020-08-12
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.2.0. [propagated-inputs]: Remove r-tsne; add r-jsonlite, r-miniui, r-shiny, r-spatstat, and r-tibble.
| * gnu: Add phast.Ricardo Wurmus2020-08-10
| | | | | | | | * gnu/packages/bioinformatics.scm (phast): New variable.
| * gnu: clipper: Update to 2.0.Ricardo Wurmus2020-08-07
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (clipper): Update to 2.0. [source]: Remove snippet. [arguments]: Build with Python 3; remove phase "fix-typo", add phase "make-files-writable". [inputs]: Replace all Python 2 variants with Python 3 variants. [native-inputs]: Add python-setuptools-git.
| * gnu: paml: Fix build.Jakub Kądziołka2020-07-30
| | | | | | | | | | * gnu/packages/bioinformatics.scm (paml)[snippet]: Fix permissions before repacking the source tarball.
* | gnu: check: Update to 0.15.1.Marius Bakke2020-07-25
|/ | | | | | | | | | | | | | | | | | * gnu/packages/check.scm (check): Update to 0.15.1. (check-0.14): New public variable. * gnu/packages/backup.scm (burp)[native-inputs]: Change from CHECK to CHECK-0.14. * gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Likewise. * gnu/packages/databases.scm (recutils)[native-inputs]: Likewise. * gnu/packages/electronics.scm (libsigrokdecode)[native-inputs]: Likewise. * gnu/packages/enlightenment.scm (efl, edi)[native-inputs]: Likewise. * gnu/packages/gnome.scm (gdm)[inputs]: Likewise. * gnu/packages/gtk.scm (girara)[native-inputs]: Likewise. * gnu/packages/messaging.scm (pidgin)[native-inputs]: Likewise. * gnu/packages/networking.scm (iodine)[native-inputs]: Likewise. * gnu/packages/pulseaudio.scm (pulseaudio)[native-inputs]: Likewise. * gnu/packages/sssd.scm (sssd)[native-inputs]: Likewise. * gnu/packages/web.scm (libwapcaplet)[native-inputs]: Likewise.
* gnu: r-rhdf5lib: Fix libsz substitution.Jakub Kądziołka2020-07-19
| | | | | | | | | This is a follow-up to commit b7f051db14fb485fcfa4917924eef186fb1b8c07 - in the new version, some of the format strings being replaced gained quotes. This commit fixes build of dependents of r-rhdf5lib, such as r-hdf5array. * gnu/packages/bioinformatics (r-rhdf5lib): Remove all instances of libsz.a.
* gnu: Use HTTPS for mdc-berlin.de home pages.Tobias Geerinckx-Rice2020-07-16
| | | | | * gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq) (pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS.
* gnu: Use HTTPS for biojava.org home pages.Tobias Geerinckx-Rice2020-07-16
| | | | | | * gnu/packages/bioinformatics.scm (java-biojava-core) (java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0) (java-biojava-alignment-4.0)[home-page]: Use HTTPS.
* gnu: r-rhdf5lib: Update to 1.10.1.Ricardo Wurmus2020-07-16
| | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
* gnu: r-qtl2: Update to 0.22-11.Ricardo Wurmus2020-07-16
| | | | * gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
* gnu: r-genomicfeatures: Update to 1.40.1.Ricardo Wurmus2020-07-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
* gnu: r-summarizedexperiment: Update to 1.18.2.Ricardo Wurmus2020-07-16
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
* gnu: r-delayedmatrixstats: Update to 1.10.1.Ricardo Wurmus2020-07-16
| | | | * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
* gnu: r-rhdf5: Update to 2.32.2.Ricardo Wurmus2020-07-16
| | | | * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2.
* gnu: Remove ".git" from "https://github/…/….git".Ludovic Courtès2020-07-12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix swh) would sometimes return #f for these because the ".git" URLs are redirects to the non-".git" URLs. Consequently, 'guix lint -c archival' would keep saying "scheduled Software Heritage archival"; likewise, the fallback download code would fail. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm, gnu/packages/android.scm, gnu/packages/animation.scm, gnu/packages/arcan.scm, gnu/packages/assembly.scm, gnu/packages/audio.scm, gnu/packages/authentication.scm, gnu/packages/avr.scm, gnu/packages/axoloti.scm, gnu/packages/backup.scm, gnu/packages/bash.scm, gnu/packages/benchmark.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/boost.scm, gnu/packages/build-tools.scm, gnu/packages/c.scm, gnu/packages/calendar.scm, gnu/packages/cdrom.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/chez.scm, gnu/packages/clojure.scm, gnu/packages/code.scm, gnu/packages/compression.scm, gnu/packages/compton.scm, gnu/packages/coq.scm, gnu/packages/cpp.scm, gnu/packages/cran.scm, gnu/packages/crypto.scm, gnu/packages/curl.scm, gnu/packages/databases.scm, gnu/packages/datastructures.scm, gnu/packages/debug.scm, gnu/packages/disk.scm, gnu/packages/distributed.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/dns.scm, gnu/packages/docker.scm, gnu/packages/education.scm, gnu/packages/efi.scm, gnu/packages/elixir.scm, gnu/packages/emacs-xyz.scm, gnu/packages/embedded.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/erlang.scm, gnu/packages/fabric-management.scm, gnu/packages/file-systems.scm, gnu/packages/finance.scm, gnu/packages/firmware.scm, gnu/packages/flashing-tools.scm, gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/fpga.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/genealogy.scm, gnu/packages/genimage.scm, gnu/packages/geo.scm, gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/gnome-xyz.scm, gnu/packages/gnome.scm, gnu/packages/gnuzilla.scm, gnu/packages/golang.scm, gnu/packages/gpodder.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/groff.scm, gnu/packages/groovy.scm, gnu/packages/gtk.scm, gnu/packages/guile-xyz.scm, gnu/packages/guile.scm, gnu/packages/hardware.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-xyz.scm, gnu/packages/hexedit.scm, gnu/packages/i2p.scm, gnu/packages/ibus.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/ipfs.scm, gnu/packages/java-graphics.scm, gnu/packages/java-maths.scm, gnu/packages/java.scm, gnu/packages/javascript.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/jupyter.scm, gnu/packages/kodi.scm, gnu/packages/language.scm, gnu/packages/lego.scm, gnu/packages/less.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm, gnu/packages/lirc.scm, gnu/packages/lisp-xyz.scm, gnu/packages/llvm.scm, gnu/packages/logging.scm, gnu/packages/lolcode.scm, gnu/packages/lua.scm, gnu/packages/lxde.scm, gnu/packages/lxqt.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/maths.scm, gnu/packages/maven.scm, gnu/packages/mes.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/node-xyz.scm, gnu/packages/ocaml.scm, gnu/packages/ocr.scm, gnu/packages/onc-rpc.scm, gnu/packages/opencl.scm, gnu/packages/opencog.scm, gnu/packages/pantheon.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/perl6.scm, gnu/packages/phabricator.scm, gnu/packages/popt.scm, gnu/packages/printers.scm, gnu/packages/prolog.scm, gnu/packages/protobuf.scm, gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/python-xyz.scm, gnu/packages/qt.scm, gnu/packages/radio.scm, gnu/packages/rails.scm, gnu/packages/rdf.scm, gnu/packages/rednotebook.scm, gnu/packages/rpc.scm, gnu/packages/rsync.scm, gnu/packages/ruby.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/screen.scm, gnu/packages/security-token.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/shellutils.scm, gnu/packages/simh.scm, gnu/packages/sml.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/stenography.scm, gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/synergy.scm, gnu/packages/telephony.scm, gnu/packages/terminals.scm, gnu/packages/tex.scm, gnu/packages/texinfo.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tmux.scm, gnu/packages/tor.scm, gnu/packages/toys.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/virtualization.scm, gnu/packages/vlang.scm, gnu/packages/vnc.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wireservice.scm, gnu/packages/wm.scm, gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm, tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
* gnu: r-annotationdbi: Update to 1.50.1.Ricardo Wurmus2020-07-02
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1.
* gnu: blast+: Update to 2.10.1.Ricardo Wurmus2020-06-30
| | | | * gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1.
* gnu: r-qtl2: Update synopsis, description.Efraim Flashner2020-06-28
| | | | | | * gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's synopsis. [description]: Same.
* gnu: r-qtl2: Update to 0.22-8.Efraim Flashner2020-06-28
| | | | | * gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8. [source]: Download from cran.
* gnu: r-scater: Update to 1.16.2.Ricardo Wurmus2020-06-28
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2.
* gnu: r-biocviews: Update to 1.56.1.Ricardo Wurmus2020-06-28
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1.
* gnu: r-dexseq: Update to 1.34.1.Ricardo Wurmus2020-06-28
| | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1.
* gnu: miniasm: Make sure all phases return #t.Efraim Flashner2020-06-23
| | | | | * gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom 'install phase return #t.
* gnu: miniasm: Don't use unstable tarball.Efraim Flashner2020-06-23
| | | | | * gnu/packages/bioinformatics.scm (miniasm)[source]: Download using git-fetch.
generated by cgit v1.2.3 (git 2.45.2) at 2024-08-08 06:02:50 +0000