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2021-02-28gnu: f-seq: Use HTTPS home page URI....* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI. Nicolas Goaziou
2021-02-23gnu: Add star-for-pigx....This is a follow-up to commit f1f6e49190a11f926af3bef0d45541cabf47c742. * gnu/packages/bioinformatics.scm (star-for-pigx): New variable. (pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx. Ricardo Wurmus
2021-02-22gnu: star: Update to 2.7.8a....* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a. Ricardo Wurmus
2021-02-19gnu: nanopolish: Fix script wrapping....* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs phase. [inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl scripts. Ricardo Wurmus
2021-02-19gnu: Add prinseq....* gnu/packages/bioinformatics.scm (prinseq): New variable. Ricardo Wurmus
2021-02-19gnu: Add ngshmmalign....* gnu/packages/bioinformatics.scm (ngshmmalign): New variable. Ricardo Wurmus
2021-02-18gnu: Add r-archr....* gnu/packages/bioinformatics.scm (r-archr): New variable. Ricardo Wurmus
2021-02-15gnu: Add indelfixer....* gnu/packages/bioinformatics.scm (indelfixer): New variable. Ricardo Wurmus
2021-02-11gnu: bowtie1: Update to 1.3.0....* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0. [arguments]: Set CC in make flags. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2021-02-11gnu: r-gage: Update to 2.40.1....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1. Ricardo Wurmus
2021-02-11gnu: r-msnbase: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1. Ricardo Wurmus
2021-02-11gnu: r-methylkit: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1. Ricardo Wurmus
2021-02-11gnu: r-delayedarray: Update to 0.16.1....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1. Ricardo Wurmus
2021-02-11gnu: r-biomart: Update to 2.46.3....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3. Ricardo Wurmus
2021-02-11gnu: r-edger: Update to 3.32.1....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1. Ricardo Wurmus
2021-02-11gnu: r-iranges: Update to 2.24.1....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1. Ricardo Wurmus
2021-02-11gnu: r-s4vectors: Update to 0.28.1....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1. Ricardo Wurmus
2021-02-11gnu: r-systempiper: Update to 1.24.3....* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3. Ricardo Wurmus
2021-02-11gnu: r-gseabase: Update to 1.52.1....* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1. Ricardo Wurmus
2021-02-11gnu: r-genefilter: Update to 1.72.1....* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1. Ricardo Wurmus
2021-02-11Merge branch 'master' into core-updatesDanny Milosavljevic
2021-02-05gnu: rsem: Link with shared libhts library....* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so instead of libhts.a. Ricardo Wurmus
2021-02-03Merge branch 'master' into core-updatesChristopher Baines
2021-02-01gnu: vcflib: Fix generated pkg-config file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom generated pkg-config file, link with all needed libraries and fix linker library. * gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly. Efraim Flashner
2021-02-01gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH....This change was automated using: $ git ls-files | grep .scm | \ xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i $ git ls-files | grep .scm | \ xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i * gnu/packages/admin.scm (nmap): (dstat): Wrap using GUIX_PYTHONPATH. * gnu/packages/audio.scm (jack-2): (carla): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (couger): Likewise. (gess, find-circ, filtlong, nanopolish): Likewise. * gnu/packages/cdrom.scm (cdemu-client): Likewise. * gnu/packages/chemistry.scm (avogadro): Likewise. * gnu/packages/connman.scm (econnman): Likewise. * gnu/packages/cups.scm (hplip): Likewise. * gnu/packages/debug.scm (scanmem): Likewise. * gnu/packages/display-managers.scm (lightdm): Likewise. * gnu/packages/ebook.scm (cozy): Likewise. * gnu/packages/education.scm (anki): Likewise. * gnu/packages/engineering.scm (kicad, volk, freecad): Likewise. * gnu/packages/game-development.scm (renpy): Likewise. * gnu/packages/games.scm (roguebox-adventures) (seahorse-adventures, kajongg): Likewise. * gnu/packages/gimp.scm (gimp, glimpse): Likewise. * gnu/packages/glib.scm (itstool): Likewise. * gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise. (eolie, d-feet, gedit, caribou, gnome-shell, authenticator) (gnome-todo, orca, passwordsafe, terminator, setzer) (libratbag, komikku): Likewise. * gnu/packages/gps.scm (gpsd): Likewise. * gnu/packages/gtk.scm (gtk-doc): Likewise. * gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy) (ibus-libhangul): Likewise. * gnu/packages/inkscape.scm (inkscape-1.0): Likewise. * gnu/packages/linux.scm (bcc): Likewise. * gnu/packages/mail.scm (notifymuch): Likewise. * gnu/packages/maths.scm (units): Likewise. * gnu/packages/music.scm (solfege): Likewise. * gnu/packages/networking.scm (blueman): Likewise. * gnu/packages/patchutils.scm (patchwork): Likewise. * gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/presentation.scm (presentty): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/storage.scm (ceph): Likewise. * gnu/packages/syndication.scm (liferea): Likewise. * gnu/packages/task-management.scm (blanket): Likewise. * gnu/packages/text-editors.scm (manuskript): Likewise. * gnu/packages/version-control.scm (gitless, cgit, git-when-merged) (git-imerge): Likewise. * gnu/packages/video.scm (pitivi): Likewise. * gnu/packages/virtualization.scm (criu): Likewise. * gnu/packages/xfce.scm (catfish): Likewise. Maxim Cournoyer
2021-02-01gnu: python-loompy: Do not set PYTHONPATH....* gnu/packages/bioinformatics.scm (python-loompy) [phases]{check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-scanpy: Do not set PYTHONPATH....* gnu/packages/bioinformatics.scm (python-scanpy)[phases] {check}: Do not set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-screed: Adjust following Python build system changes....* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no longer necessary. Maxim Cournoyer
2021-02-01gnu: bamm: Update following changes to the Python build system....* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t. [phases]{check}: Override rather than delete phase. Remove trailing #t. {post-install-check}: Delete phase. {wrap-executable}: Also wrap with the new GUIX_PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-pysam: Adjust following Python build system changes....* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the '#:modules' argument. [phases]: Remove trailing #t. {check}: Do not manually set PYTHONPATH. Maxim Cournoyer
2021-02-01gnu: python-pybedtools: Streamline following Python build system changes....* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t. [phases]{check}: Do not manually set PYTHONPATH. [arguments]: Remove the '#:modules' argument. Maxim Cournoyer
2021-01-29gnu: Replace all uses of texlive-union by texlive-updmap.cfg....* doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg. * gnu/packages/algebra.scm (pari-gp): Likewise. * gnu/packages/bioinformatics.scm (discrover, velvet): Likewise. * gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise. * gnu/packages/docbook.scm (dblatex): Likewise. * gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise. * gnu/packages/engineering.scm (fastcap): Likewise. * gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise. * gnu/packages/lisp.scm (sbcl): Likewise. * gnu/packages/maths.scm (octave, hypre): Likewise. * gnu/packages/music.scm (lilypond): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation) (python-matplotlib-documentation, python-ipython-documentation) (python-pypandoc): Likewise. * gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise. * gnu/packages/scheme.scm (mit-scheme): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/tex.scm (simple-texlive-package) (texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise. Maxim Cournoyer
2021-01-29gnu: grocsvs: Remove package....This package depends on Python 2 and doesn't build anymore. Upstream doesn't seem active, but if they ever port it to Python 3, they should let people know here: https://github.com/grocsvs/grocsvs/issues/6. * gnu/packages/bioinformatics.scm (grocsvs): Delete. Maxim Cournoyer
2021-01-28gnu: Add r-demultiplex....* gnu/packages/bioinformatics.scm (r-demultiplex): New variable. Ricardo Wurmus
2021-01-28gnu: Add repeat-masker....* gnu/packages/bioinformatics.scm (repeat-masker): New variable. Ricardo Wurmus
2021-01-28gnu: Add trf....* gnu/packages/bioinformatics.scm (trf): New variable. Ricardo Wurmus
2021-01-19gnu: freebayes: Update source, home-page URIs....* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new upstream URI. [home-page]: Same. Efraim Flashner
2021-01-19gnu: freebayes: Don't include vcflib sources....* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove vcflib-source, intervaltree-source. Move vcflib ... [inputs]: ... to here. [arguments]: Adjust 'patch-source and 'unpack-submodule-sources for changes in vendored code. * gnu/packages/patches/freebayes-devendor-deps.patch: Update patch. Efraim Flashner
2021-01-19gnu: vcflib: Add pkg-config file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to create pkg-config file. Efraim Flashner
2021-01-19gnu: vcflib: Build a shared library....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to build a shared library instead of a static one. Efraim Flashner
2021-01-19gnu: freebayes: Extend test timeout on slower architectures....* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom 'check phase on aarch64-linux and armhf-linux to extend the test timeout. Efraim Flashner
2021-01-18gnu: Add r-snapatac....* gnu/packages/bioinformatics.scm (r-snapatac): New variable. Mădălin Ionel Patrașcu
2021-01-18gnu: mafft: Update to 7.475....* gnu/packages/bioinformatics.scm (mafft): Update to 7.475. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Mădălin Ionel Patrașcu
2021-01-18gnu: ruby-bio-vcf: Rename to bio-vcf....This package is widely known in select circles specifically as 'bio-vcf'. * gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf. Efraim Flashner
2021-01-18gnu: Add ruby-bio-vcf....* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable. Efraim Flashner
2021-01-17gnu: freebayes: Update to 1.3.3....* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3. [source]: Add patch. Add snippet to remove vendored library. [build-system]: Switch to meson-build-system. [inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp. [native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman source, multichoose source, fsom source, filevercmp source, fastahack source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib. [arguments]: Drop make-flags. Don't delete 'configure phase. Delete custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install phases. Adjust 'unpack-submodule-sources phase to changed native-inputs. Add new 'patch-source phase. Efraim Flashner
2021-01-17gnu: multichoose: Install header files....* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust 'install phase to also install header files. Efraim Flashner
2021-01-17gnu: filevercmp: Install header files....* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust 'install phase to install header files. Efraim Flashner
2021-01-14gnu: vcflib: Update to 1.0.2....* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2. [source]: Download using git-fetch. Remove patch. Update snippet to use packaged libraries. [build-system]: Switch to cmake-build-system. [inputs]: Add bzip2. [native-inputs]: Add package-source of fsom. [arguments]: Delete custom 'set-flags, 'install phases. Don't delete 'configure phase. Adjust 'unpack-submodule-sources phase. * gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Efraim Flashner
2021-01-14gnu: sambamba Update to 0.8.0....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0. [source, home-page]: Update to new upstream URI. [arguments]: Shorten 'fix-ldc-version phase. Remove 'place-biod-and-undead phase. Update 'unbundle-prerequisites and 'insatll phases. [native-inputs]: Remove rdmd, biod. Move ldc ... [inputs]: ... to here. Add zlib. (htslib-for-sambamba): Remove variable. Efraim Flashner
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