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2020-09-05gnu: seqmagick: Update to 0.8.0....* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0. Andreas Enge
2020-08-30gnu: delly: Update to 0.8.3....* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3. [inputs]: Order alphabetically. Efraim Flashner
2020-08-27gnu: vcflib: Install pkgconfig file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom 'install phase to add vcflib.pc. Efraim Flashner
2020-08-27gnu: vcflib: Use shared libraries....* 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. Efraim Flashner
2020-08-27gnu: fastahack: Install pkgconfig file....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom 'install phase to add fastahack.pc. Efraim Flashner
2020-08-27gnu: fastahack: Build and install shared library and headers....* 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. Efraim Flashner
2020-08-27gnu: smithwaterman: Install pkgconfig file....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust custom 'install phase to add smithwaterman.pc file. Efraim Flashner
2020-08-27gnu: smithwaterman: Build and install shared library and headers....* 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. Efraim Flashner
2020-08-27gnu: tabixpp: Install pkgconfig file....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom 'install phase to add tabixpp.pc file. Efraim Flashner
2020-08-27gnu: tabixpp: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom 'build phase to build shared library. Adjust custom 'install phase to install libraries and header. Efraim Flashner
2020-08-20gnu: r-complexheatmap: Update to 2.4.3....* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3. Ricardo Wurmus
2020-08-20gnu: r-gage: Update to 2.38.3....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3. [propagated-inputs]: Add r-go-db. Ricardo Wurmus
2020-08-20gnu: r-annotationhub: Update to 2.20.2....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2. Ricardo Wurmus
2020-08-20gnu: r-delayedarray: Update to 0.14.1....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1. Ricardo Wurmus
2020-08-20gnu: r-annotationdbi: Update to 1.50.3....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3. Ricardo Wurmus
2020-08-20gnu: r-biocviews: Update to 1.56.2....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2. Ricardo Wurmus
2020-08-19gnu: pigx-chipseq: Update to 0.0.43....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43. Ricardo Wurmus
2020-08-18gnu: bowtie1: Add missing Python input....Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de> * gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper. Ricardo Wurmus
2020-08-16gnu: pigx-bsseq: Update to 0.1.2....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2. [inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster. Ricardo Wurmus
2020-08-16gnu: pigx-scrnaseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc. Ricardo Wurmus
2020-08-16gnu: pigx-bsseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc. Ricardo Wurmus
2020-08-16gnu: pigx-chipseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc. Ricardo Wurmus
2020-08-16gnu: pigx-rnaseq: Use statically linked Pandoc....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Use pandoc and pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc. Ricardo Wurmus
2020-08-16gnu: r-rcas: Use pandoc instead of ghc-pandoc....* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Replace ghc-pandoc with pandoc. Ricardo Wurmus
2020-08-15gnu: hisat2: Use pandoc instead of ghc-pandoc....* gnu/packages/bioinformatics.scm (hisat2)[native-inputs]: Replace ghc-pandoc with pandoc. Ricardo Wurmus
2020-08-12gnu: tophat: Hide default GCC....* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase "hide-default-gcc". Ricardo Wurmus
2020-08-12gnu: r-seurat: Update to 3.2.0....* 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. Ricardo Wurmus
2020-08-10gnu: Add phast....* gnu/packages/bioinformatics.scm (phast): New variable. Ricardo Wurmus
2020-08-07gnu: clipper: Update to 2.0....* 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. Ricardo Wurmus
2020-07-30gnu: paml: Fix build....* gnu/packages/bioinformatics.scm (paml)[snippet]: Fix permissions before repacking the source tarball. Jakub Kądziołka
2020-07-19gnu: r-rhdf5lib: Fix libsz substitution....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. Jakub Kądziołka
2020-07-16gnu: Use HTTPS for mdc-berlin.de home pages....* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq) (pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2020-07-16gnu: Use HTTPS for biojava.org home pages....* 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. Tobias Geerinckx-Rice
2020-07-16gnu: r-rhdf5lib: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1. Ricardo Wurmus
2020-07-16gnu: r-qtl2: Update to 0.22-11....* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11. Ricardo Wurmus
2020-07-16gnu: r-genomicfeatures: Update to 1.40.1....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1. Ricardo Wurmus
2020-07-16gnu: r-summarizedexperiment: Update to 1.18.2....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2. Ricardo Wurmus
2020-07-16gnu: r-delayedmatrixstats: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1. Ricardo Wurmus
2020-07-16gnu: r-rhdf5: Update to 2.32.2....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2. Ricardo Wurmus
2020-07-12gnu: Remove ".git" from "https://github/…/….git"....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. Ludovic Courtès
2020-07-02gnu: r-annotationdbi: Update to 1.50.1....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1. Ricardo Wurmus
2020-06-30gnu: blast+: Update to 2.10.1....* gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1. Ricardo Wurmus
2020-06-28gnu: r-qtl2: Update synopsis, description....* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's synopsis. [description]: Same. Efraim Flashner
2020-06-28gnu: r-qtl2: Update to 0.22-8....* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8. [source]: Download from cran. Efraim Flashner
2020-06-28gnu: r-scater: Update to 1.16.2....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2. Ricardo Wurmus
2020-06-28gnu: r-biocviews: Update to 1.56.1....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1. Ricardo Wurmus
2020-06-28gnu: r-dexseq: Update to 1.34.1....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1. Ricardo Wurmus
2020-06-23gnu: miniasm: Make sure all phases return #t....* gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom 'install phase return #t. Efraim Flashner
2020-06-23gnu: miniasm: Don't use unstable tarball....* gnu/packages/bioinformatics.scm (miniasm)[source]: Download using git-fetch. Efraim Flashner
2020-06-22gnu: python-plotly: Update to 4.8.1....But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pierre Langlois
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