Commit Graph

3440 Commits

Author SHA1 Message Date
Mădălin Ionel Patrașcu
60652a8efa
gnu: Add r-p2data.
* gnu/packages/bioinformatics.scm (r-p2data): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-03-01 14:07:58 +01:00
Mădălin Ionel Patrașcu
df74c74688
gnu: Add r-conospanel.
* gnu/packages/bioinformatics.scm (r-conospanel): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-03-01 14:06:04 +01:00
Lars-Dominik Braun
baf9e0a336
gnu: ngless: Drop Haskell libraries and documentation.
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Add
'remove-libraries phase and disable #:haddock?.
2023-02-26 10:26:16 +01:00
Lars-Dominik Braun
49a320aaa6
Upgrade Haskell packages.
Script-aided bulk change.
2023-02-26 10:26:07 +01:00
Tobias Geerinckx-Rice
1e6ddceb83
gnu: Use HTTPS package home pages wherever possible.
* gnu/packages/accessibility.scm (florence)[home-page]: Use HTTPS.
* gnu/packages/admin.scm (netcat, nmon)[home-page]: Likewise.
* gnu/packages/algebra.scm (mpfrcx, cm, flint, fftw, r-dtt)[home-page]:
Likewise.
* gnu/packages/apr.scm (apr, apr-util)[home-page]: Likewise.
* gnu/packages/aspell.scm (aspell-dict-it)[home-page]: Likewise.
* gnu/packages/astronomy.scm (casacore, sextractor, libnova)
(xplanet)[home-page]: Likewise.
* gnu/packages/audio.scm (libtimidity, alsa-modular-synth, azr3, tao)
(freepats, rakarrack, liblo, libshout-idjc, timidity++, libsbsms)
(libmodplug, libxmp, xmp, sox, drc, gsm, gnaural)
(streamripper)[home-page]: Likewise.
* gnu/packages/authentication.scm (pamtester)[home-page]: Likewise.
* gnu/packages/backup.scm (grsync)[home-page]: Likewise.
* gnu/packages/bioconductor.scm (r-nmf, r-edger, r-limma)
(r-plgem)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (python-biom-format, bowtie, bowtie1)
(bwa, crossmap, java-htsjdk, java-htsjdk-latest, java-picard)
(java-picard-2.10.3, kaiju, proteinortho, rsem, rseqc, seek, samtools)
(snap-aligner, subread, stringtie, r-centipede, prinseq, emboss, phylip)
(libsbml)[home-page]: Likewise.
* gnu/packages/build-tools.scm (tup)[home-page]: Likewise.
* gnu/packages/cdrom.scm (libcddb, cdrdao, cdrtools)
(cd-discid)[home-page]: Likewise.
* gnu/packages/check.scm (cunit, python-nose)
(python-pyhamcrest)[home-page]: Likewise.
* gnu/packages/chemistry.scm (gromacs)[home-page]: Likewise.
* gnu/packages/chez.scm (chez-fmt)[home-page]: Likewise.
* gnu/packages/code.scm (lcov, uncrustify, cscope)[home-page]: Likewise.
* gnu/packages/compression.scm (p7zip)[home-page]: Likewise.
* gnu/packages/cran.scm (r-emdist, r-proj4, r-zoo, r-ggalluvial)
(r-orgmassspecr, r-polychrome, r-partykit, r-rcpp, r-ff, r-emdbook)
(r-fitdistrplus, r-linprog, r-geometry, r-dtw, r-fst, r-rjags)
(r-intergraph, r-qualv, r-labelled, r-survey, r-coin, r-fmsb, r-tm)
(r-corpcor, r-rmpfr, r-spatialextremes, r-longitudinal, r-genenet)
(r-bayesm, r-seqinr, r-mpm, r-text2vec, r-rgdal, r-seewave, r-hdrcde)
(r-shapes, r-anytime, r-stm, r-d3network, r-tam, r-directlabels)
(r-spatstat-utils, r-spatstat-sparse, r-spatstat-data, r-spatstat-geom)
(r-spatstat-core, r-spatstat-linnet, r-spatstat-random, r-spatstat)
(r-rcpptoml, r-mlecens, r-seurat, r-mlearning, r-zooimage)[home-page]:
Likewise.
* gnu/packages/crates-io.scm (rust-nickel-0.11, rust-thrift-0.13)
(rust-trust-dns-https-0.20, rust-trust-dns-native-tls-0.20)
(rust-trust-dns-openssl-0.20, rust-trust-dns-proto-0.20)
(rust-trust-dns-resolver-0.20, rust-trust-dns-rustls-0.20)
(rust-uint-0.9, rust-yaml-rust-0.4)[home-page]: Likewise.
* gnu/packages/crypto.scm (libdecaf, ccrypt)[home-page]: Likewise.
* gnu/packages/curl.scm (curlpp)[home-page]: Likewise.
* gnu/packages/databases.scm (python-pylibmc, unixodbc, wiredtiger)
(libpqxx, mdbtools, virtuoso-ose, libdbi, libdbi-drivers)
(soci)[home-page]: Likewise.
* gnu/packages/debian.scm (apt-mirror)[home-page]: Likewise.
* gnu/packages/debug.scm (remake)[home-page]: Likewise.
* gnu/packages/disk.scm (sdparm, idle3-tools, duc)[home-page]: Likewise.
* gnu/packages/django.scm (python-django-haystack)[home-page]: Likewise.
* gnu/packages/djvu.scm (djvulibre, djview)[home-page]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[home-page]: Likewise.
* gnu/packages/docbook.scm (dblatex, docbook2x)[home-page]: Likewise.
* gnu/packages/documentation.scm (scrollkeeper)[home-page]: Likewise.
* gnu/packages/ebook.scm (liblinebreak)[home-page]: Likewise.
* gnu/packages/electronics.scm (xoscope)[home-page]: Likewise.
* gnu/packages/emacs-xyz.scm (emacs-bbdb, emacs-caps-lock, emacs-djvu)
(emacs-pabbrev, emacs-twittering-mode, emacs-filladapt, emacs-rudel)
(emacs-stream, emacspeak, emacs-cc-mode, emacs-eldoc, emacs-jsonrpc)
(emacs-gtk-look, emacs-xclip, emacs-slime-volleyball, emacs-minimap)
(emacs-auto-dictionary-mode, emacs-persist, emacs-shell-command+)
(emacs-map, emacs-xref, emacs-dictionary)[home-page]: Likewise.
* gnu/packages/embedded.scm (sdcc)[home-page]: Likewise.
* gnu/packages/engineering.scm (asco, libngspice, libspnav)
(openctm)[home-page]: Likewise.
* gnu/packages/erlang.scm (erlang-erlware-commons)[home-page]: Likewise.
* gnu/packages/file-systems.scm (jfsutils, curlftpfs)[home-page]:
Likewise.
* gnu/packages/finance.scm (gbonds)[home-page]: Likewise.
* gnu/packages/flashing-tools.scm (dfu-util, srecord)[home-page]:
Likewise.
* gnu/packages/fltk.scm (ntk)[home-page]: Likewise.
* gnu/packages/fonts.scm (font-terminus, font-tex-gyre)
(font-comic-neue)[home-page]: Likewise.
* gnu/packages/fontutils.scm (ttf2pt1, potrace, libspiro)[home-page]:
Likewise.
* gnu/packages/fpga.scm (icestorm, gtkwave, gtkwave)
(python-myhdl)[home-page]: Likewise.
* gnu/packages/freedesktop.scm (libatasmart)[home-page]: Likewise.
* gnu/packages/ftp.scm (weex)[home-page]: Likewise.
* gnu/packages/game-development.scm (dds, python-tmx, sfxr, quesoglc)
(eureka, plib)[home-page]: Likewise.
* gnu/packages/games.scm (abe, alex4, armagetronad, barony)
(foobillard++, golly, ltris, pipewalker, prboom-plus, trigger-rally)
(cmatrix, pinball, pioneers, tennix, chromium-bsu, freeciv, kiki)
(quakespasm, frotz, frotz-dumb-terminal, frotz-sdl, btanks)
(flare-engine, chessx, barrage, cgoban, passage)[home-page]: Likewise.
* gnu/packages/geo.scm (python-geopandas, saga)[home-page]: Likewise.
* gnu/packages/gl.scm (freeglut, gl2ps)[home-page]: Likewise.
* gnu/packages/gnome.scm (cogl, clutter-gtk, clutter-gst, bluefish)
(workrave)[home-page]: Likewise.
* gnu/packages/gnustep.scm (wmnd, wmfire, wmfire)[home-page]: Likewise.
* gnu/packages/graph.scm (mscgen)[home-page]: Likewise.
* gnu/packages/graphics.scm (assimp, alembic, ctl, agg)
(opencsg)[home-page]: Likewise.
* gnu/packages/graphviz.scm (gts)[home-page]: Likewise.
* gnu/packages/gtk.scm (gtkspell3)[home-page]: Likewise.
* gnu/packages/guile-xyz.scm (guile-irregex)[home-page]: Likewise.
* gnu/packages/haskell-apps.scm (cpphs)[home-page]: Likewise.
* gnu/packages/haskell-check.scm (ghc-hunit)[home-page]: Likewise.
* gnu/packages/haskell-web.scm (ghc-http-client-restricted)
(ghc-blaze-html, ghc-happstack-server, ghc-sourcemap)[home-page]:
Likewise.
* gnu/packages/haskell-xyz.scm (ghc-assoc, ghc-cairo, ghc-cborg)
(ghc-csv, ghc-glob, ghc-gtk2hs-buildtools, ghc-hmatrix-gsl-stats)
(ghc-intervalmap, ghc-lens-family-core, ghc-managed, ghc-mountpoints)
(ghc-network-multicast, ghc-optional-args, ghc-regex, ghc-spoon)
(ghc-transformers, ghc-turtle, ghc-utf8-light, ghc-wizards)
(ghc-template-haskell, ghc-boot-th, ghc-binary-orphans)
(ghc-postgresql-simple)[home-page]: Likewise.
* gnu/packages/hexedit.scm (ht, bvi)[home-page]: Likewise.
* gnu/packages/hunspell.scm (hunspell-dict-hu)[home-page]: Likewise.
* gnu/packages/image-processing.scm (mia)[home-page]: Likewise.
* gnu/packages/image-viewers.scm (geeqie, gpicview, luminance-hdr)
(qiv)[home-page]: Likewise.
* gnu/packages/image.scm (libuemf, devil, steghide, optipng, niftilib)
(sng, mtpaint)[home-page]: Likewise.
* gnu/packages/java-xml.scm (java-simple-xml, java-jaxp)
(java-apache-xml-commons-resolver)[home-page]: Likewise.
* gnu/packages/java.scm (java-cisd-base, java-cisd-args4j)
(java-hamcrest-core, java-jsr305, java-eclipse-osgi)
(java-eclipse-equinox-common, java-eclipse-core-jobs)
(java-eclipse-equinox-registry, java-eclipse-equinox-app)
(java-eclipse-equinox-preferences, java-eclipse-core-contenttype)
(java-eclipse-text, java-treelayout, java-aopalliance, java-jeromq)
(java-cdi-api)[home-page]: Likewise.
* gnu/packages/jemalloc.scm (jemalloc-4.5.0)[home-page]: Likewise.
* gnu/packages/julia-xyz.scm (julia-recipespipeline)[home-page]:
Likewise.
* gnu/packages/kde-internet.scm (kget)[home-page]: Likewise.
* gnu/packages/kde-systemtools.scm (dolphin-plugins)
(konsole)[home-page]: Likewise.
* gnu/packages/kodi.scm (fstrcmp)[home-page]: Likewise.
* gnu/packages/language.scm (hime, libchewing)[home-page]: Likewise.
* gnu/packages/lego.scm (nqc)[home-page]: Likewise.
* gnu/packages/lesstif.scm (lesstif)[home-page]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[home-page]: Likewise.
* gnu/packages/libdaemon.scm (libdaemon)[home-page]: Likewise.
* gnu/packages/libffi.scm (libffi)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (libwpd, libwpg, libwps)[home-page]:
Likewise.
* gnu/packages/libusb.scm (libmtp, gmtp)[home-page]: Likewise.
* gnu/packages/linux.scm (e2fsprogs, extundelete, lsscsi, net-tools)
(kbd, sysfsutils, cpuid, libpfm4)[home-page]: Likewise.
* gnu/packages/lisp-check.scm (sbcl-ptester, sbcl-xlunit)[home-page]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-html-encode, sbcl-py-configparser)
(sbcl-cl-utilities, sbcl-series, sbcl-uffi, sbcl-clsql, sbcl-sycamore)
(sbcl-osicat, sbcl-hu.dwim.common, sbcl-caveman, sbcl-trivial-shell)
(sbcl-trivial-benchmark, sbcl-screamer, sbcl-smug)[home-page]: Likewise.
* gnu/packages/lisp.scm (lush2)[home-page]: Likewise.
* gnu/packages/logging.scm (log4cpp)[home-page]: Likewise.
* gnu/packages/lua.scm (lua-ldoc)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (mcl, openfst, rxcpp)[home-page]:
Likewise.
* gnu/packages/mail.scm (muchsync, procmail, sendmail)
(opensmtpd-filter-dkimsign, crm114)[home-page]: Likewise.
* gnu/packages/man.scm (libpipeline, man-db)[home-page]: Likewise.
* gnu/packages/maths.scm (lapack, scalapack, hdf-eos5, itpp, gmsh)
(metamath, p4est, armadillo, suitesparse, atlas, lpsolve, wcalc, why3)
(frama-c)[home-page]: Likewise.
* gnu/packages/mcrypt.scm (mcrypt, libmcrypt, libmhash)[home-page]:
Likewise.
* gnu/packages/minetest.scm (minetest-advtrains)[home-page]: Likewise.
* gnu/packages/monitoring.scm (python-whisper, python-carbon)
(hostscope)[home-page]: Likewise.
* gnu/packages/mp3.scm (id3lib, libmp3splt, mp3splt, mpg321)
(lame)[home-page]: Likewise.
* gnu/packages/multiprecision.scm (mpc)[home-page]: Likewise.
* gnu/packages/music.scm (aria-maestosa, lingot, setbfree, bristol)
(portmidi, python-pyportmidi, zynaddsubfx, yoshimi, aj-snapshot)
(schismtracker, midicsv, midicsv, qmidiarp, qmidiroute, dssi, tap-lv2)
(shiru-lv2)[home-page]: Likewise.
* gnu/packages/ncurses.scm (stfl)[home-page]: Likewise.
* gnu/packages/networking.scm (lksctp-tools, mbuffer, ifstatus, bird)
(tunctl, traceroute)[home-page]: Likewise.
* gnu/packages/node-xyz.scm (node-mersenne)[home-page]: Likewise.
* gnu/packages/ntp.scm (openntpd)[home-page]: Likewise.
* gnu/packages/ocaml.scm (opam, hevea, ocaml-menhir, ocaml-piqilib)
(ocaml-graph, cubicle)[home-page]: Likewise.
* gnu/packages/opencl.scm (python-pyopencl)[home-page]: Likewise.
* gnu/packages/package-management.scm (xstow, modules)[home-page]:
Likewise.
* gnu/packages/parallel.scm (xjobs)[home-page]: Likewise.
* gnu/packages/pdf.scm (podofo, qpdf, xournal, impressive)[home-page]:
Likewise.
* gnu/packages/perl.scm (perl-math-vecstat, perltidy)[home-page]:
Likewise.
* gnu/packages/photo.scm (libpano13, enblend-enfuse, hugin)[home-page]:
Likewise.
* gnu/packages/plan9.scm (drawterm)[home-page]: Likewise.
* gnu/packages/plotutils.scm (guile-charting, ploticus)[home-page]:
Likewise.
* gnu/packages/popt.scm (argtable, popt)[home-page]: Likewise.
* gnu/packages/profiling.scm (otf2)[home-page]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[home-page]: Likewise.
* gnu/packages/python-check.scm (python-mypy)[home-page]: Likewise.
* gnu/packages/python-web.scm (python-cssutils)
(python-translationstring)[home-page]: Likewise.
* gnu/packages/python-xyz.scm (python-diskcache, python-doxyqml)
(python-docutils, python-pexpect, python-importlib-resources)
(python-simplegeneric, python-urwid, python-xlrd, python-xlwt)
(python-pyasn1, python-pythondialog, python-tftpy, python-random2)
(python-arcp, python-pyopengl, python-sortedcollections)
(python-sortedcontainers, python-yapsy, python-pydispatcher)
(python-posix-ipc)[home-page]: Likewise.
* gnu/packages/qt.scm (qwt, libqglviewer, signond)[home-page]: Likewise.
* gnu/packages/radio.scm (unixcw, gnuais)[home-page]: Likewise.
* gnu/packages/raspberry-pi.scm (bcm2835)[home-page]: Likewise.
* gnu/packages/rdf.scm (clucene, rasqal, redland)[home-page]: Likewise.
* gnu/packages/regex.scm (tre)[home-page]: Likewise.
* gnu/packages/rsync.scm (librsync)[home-page]: Likewise.
* gnu/packages/ruby.scm (ruby-packnga, ruby-nokogiri, ruby-oj, ruby-ox)
(ruby-sinatra, ruby-citrus, ruby-cbor, ruby-roda)[home-page]: Likewise.
* gnu/packages/scheme.scm (scheme48, tinyscheme)[home-page]: Likewise.
* gnu/packages/screen.scm (dtach)[home-page]: Likewise.
* gnu/packages/scsi.scm (sg3-utils)[home-page]: Likewise.
* gnu/packages/sdl.scm (libmikmod, sdl-pango)[home-page]: Likewise.
* gnu/packages/shellutils.scm (hstr, rig)[home-page]: Likewise.
* gnu/packages/simulation.scm (python-dolfin-adjoint)[home-page]:
Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[home-page]: Likewise.
* gnu/packages/speech.scm (espeak)[home-page]: Likewise.
* gnu/packages/stalonetray.scm (stalonetray)[home-page]: Likewise.
* gnu/packages/statistics.scm (jags, r-mass, r-class, r-lattice)
(r-matrix, r-nnet, r-spatial, r-bit, r-bit64, r-digest, r-xtable)
(python-statsmodels, r-ade4, r-latticeextra, r-rcurl, r-xml, r-mvtnorm)
(r-robustbase, r-minqa, r-fdrtool, java-jdistlib, xlispstat)[home-page]:
Likewise.
* gnu/packages/swig.scm (swig)[home-page]: Likewise.
* gnu/packages/task-management.scm (wtime)[home-page]: Likewise.
* gnu/packages/tcl.scm (itcl, tclxml, tclx)[home-page]: Likewise.
* gnu/packages/terminals.scm (libtermkey, mlterm, libvterm)
(libvterm)[home-page]: Likewise.
* gnu/packages/tex.scm (texlive-lm, texlive-lm-math, texlive-cs)
(texlive-csplain, biber, texmaker)[home-page]: Likewise.
* gnu/packages/text-editors.scm (joe)[home-page]: Likewise.
* gnu/packages/textutils.scm (drm-tools, docx2txt)[home-page]: Likewise.
* gnu/packages/tv.scm (tvtime)[home-page]: Likewise.
* gnu/packages/unicode.scm (libunibreak)[home-page]: Likewise.
* gnu/packages/upnp.scm (libupnp)[home-page]: Likewise.
* gnu/packages/version-control.scm (cvs)[home-page]: Likewise.
* gnu/packages/video.scm (transcode, libquicktime, mjpegtools, aalib)
(liba52, libmpeg2, x265, libdv, dvdauthor, aegisub, pitivi, gavl)
(dvdbackup, guvcview, video-contact-sheet)[home-page]: Likewise.
* gnu/packages/virtualization.scm (bochs)[home-page]: Likewise.
* gnu/packages/w3m.scm (w3m)[home-page]: Likewise.
* gnu/packages/web.scm (qjson, libquvi-scripts, libquvi, quvi)
(tidy-html, htmlcxx)[home-page]: Likewise.
* gnu/packages/wm.scm (evilwm, menumaker)[home-page]: Likewise.
* gnu/packages/wv.scm (wv)[home-page]: Likewise.
* gnu/packages/wxwidgets.scm (wxsvg)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (mtdev, xsel)[home-page]: Likewise.
* gnu/packages/xfig.scm (xfig, transfig)[home-page]: Likewise.
* gnu/packages/xml.scm (openjade, python-pyxb, xmlstarlet, xmlrpc-c)
(opensp)[home-page]: Likewise.
* gnu/packages/xorg.scm (xf86-video-qxl)[home-page]: Likewise.
2023-02-19 01:00:01 +01:00
Efraim Flashner
672036c6df
gnu: Remove unneeded module imports.
* gnu/packages/abiword.scm,
* gnu/packages/ada.scm,
* gnu/packages/agda.scm,
* gnu/packages/backup.scm,
* gnu/packages/barrier.scm,
* gnu/packages/bioinformatics.scm,
* gnu/packages/bootstrap.scm,
* gnu/packages/bqn.scm,
* gnu/packages/c.scm,
* gnu/packages/chemistry.scm,
* gnu/packages/coq.scm,
* gnu/packages/cross-base.scm,
* gnu/packages/databases.scm,
* gnu/packages/emacs-xyz.scm,
* gnu/packages/enlightenment.scm,
* gnu/packages/games.scm,
* gnu/packages/geo.scm,
* gnu/packages/ghostscript.scm,
* gnu/packages/gl.scm,
* gnu/packages/golang.scm,
* gnu/packages/jami.scm,
* gnu/packages/java-maths.scm,
* gnu/packages/kde-frameworks.scm,
* gnu/packages/kde-plasma.scm,
* gnu/packages/language.scm,
* gnu/packages/libreoffice.scm,
* gnu/packages/linphone.scm,
* gnu/packages/lisp.scm,
* gnu/packages/llvm.scm,
* gnu/packages/machine-learning.scm,
* gnu/packages/minetest.scm,
* gnu/packages/monitoring.scm,
* gnu/packages/nfs.scm,
* gnu/packages/ocr.scm,
* gnu/packages/opencl.scm,
* gnu/packages/pdf.scm,
* gnu/packages/python-xyz.scm,
* gnu/packages/racket.scm,
* gnu/packages/rust.scm,
* gnu/packages/syncthing.scm,
* gnu/packages/syndication.scm,
* gnu/packages/telegram.scm,
* gnu/packages/vulkan.scm,
* gnu/packages/web-browsers.scm,
* gnu/packages/web.scm,
* gnu/packages/webkit.scm: Remove some unecessary module imports.
2023-02-16 22:41:03 +02:00
Ricardo Wurmus
b6a4fbb488
gnu: fastqc: Update to 0.11.9.
* gnu/packages/bioinformatics.scm (fastqc): Update to 0.11.9.
[source]: Fetch via git; delete bundled jar files.
[arguments]: Also patch .classpath file in 'fix-dependencies; fix patching of
reference to java in fastqc wrapper; override CLASSPATH.
2023-02-16 16:56:10 +01:00
Ricardo Wurmus
67d2f688fb
gnu: jellyfish: Remove confusing quoting syntax.
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Do not mix
quasiquote with gexp.
2023-02-13 23:09:23 +01:00
Ricardo Wurmus
661e995c70
gnu: jellyfish: Drop input labels.
* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Drop package
labels.
2023-02-13 23:09:23 +01:00
Ricardo Wurmus
4ef9ac7f27
gnu: fastp: Update to 0.23.2.
* gnu/packages/bioinformatics.scm (fastp): Update to 0.23.2.
[inputs]: Remove zlib; add isa-l and libdeflate.
2023-02-13 23:09:23 +01:00
Ricardo Wurmus
54b431b7b3
gnu: fastp: Simplify.
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Simplify gexp.
2023-02-13 23:09:23 +01:00
Ricardo Wurmus
7260cc75da
gnu: fastqc: Use gexp.
* gnu/packages/bioinformatics.scm (fastqc)[arguments]: Use gexp; drop
trailing #T from build phase.
[inputs]: Drop package labels.
2023-02-13 23:09:23 +01:00
Efraim Flashner
48903df6cb
gnu: go-github-com-biogo-hts-bam: Update to 1.4.4.
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): Update
to 1.4.4.
2023-02-11 19:05:02 +02:00
Ricardo Wurmus
8a0b625a2d
gnu: scregseg: Update to 0.1.3.
* gnu/packages/bioinformatics.scm (scregseg): Update to 0.1.3.
[source]: Simplify snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Add phases 'set-numba-cache-dir and 'build-extensions; enable
tests.
2023-02-10 19:41:54 +01:00
Ricardo Wurmus
fea66096a2
gnu: Add python-doubletdetection.
* gnu/packages/bioinformatics.scm (python-doubletdetection): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2023-02-10 19:36:36 +01:00
Ricardo Wurmus
8340acfa5a
gnu: Add python-phenograph.
* gnu/packages/bioinformatics.scm (python-phenograph): New variable.
2023-02-10 19:36:29 +01:00
Ricardo Wurmus
769346eef7
gnu: Add louvain.
* gnu/packages/bioinformatics.scm (louvain): New variable.
2023-02-10 15:48:51 +01:00
Navid Afkhami
4d35a5e2b6
gnu: Add python-scrublet.
* gnu/packages/bioinformatics.scm (python-scrublet): New variable.
2023-02-09 11:05:29 +01:00
Navid Afkhami
532dace22d
gnu: Add bitmapperbs.
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-02-07 19:38:44 +01:00
Ricardo Wurmus
a083a9b512
Revert "gnu: Add bitmapperbs."
This reverts commit f55cc9cb0f.
This commit was prematurely pushed.
2023-02-07 15:36:21 +01:00
Navid Afkhami
f55cc9cb0f
gnu: Add bitmapperbs.
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
2023-02-07 15:04:12 +01:00
Ricardo Wurmus
a582d86346
gnu: Add r-ggsankey.
* gnu/packages/bioinformatics.scm (r-ggsankey): New variable.
2023-02-06 10:52:24 +01:00
Navid Afkhami
a60c750eec
gnu: Add r-psupertime.
* gnu/packages/bioinformatics.scm (r-psupertime): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-02-03 16:57:00 +01:00
Navid Afkhami
59b102cab9
gnu: Add python-demuxem.
* gnu/packages/bioinformatics.scm (python-demuxem): New variable.
2023-02-03 11:34:42 +01:00
Navid Afkhami
89d76adf98
gnu: Add python-pegasusio.
* gnu/packages/bioinformatics.scm (python-pegasusio): New variable.
2023-02-03 11:34:42 +01:00
Navid Afkhami
ef879d7f40
gnu: Add r-streamgraph.
* gnu/packages/bioinformatics.scm (r-streamgraph): New variable.
2023-02-03 11:34:38 +01:00
Tor-björn Claesson
a84ceaa8b2
gnu: gdcm: Add documentation.
* gnu/packages/bioinformatics.scm (gdcm)[outputs]: New field.
[arguments]: Add #:phases.  Augment #:configure-flags.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-25 23:50:42 +01:00
Tor-björn Claesson
56551281a5
gnu: gdcm: Ignore 3 failing tests.
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more
failing tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-25 23:50:42 +01:00
Ricardo Wurmus
0d713e0140
gnu: Add python-slamdunk.
* gnu/packages/bioinformatics.scm (python-slamdunk): New variable.
2023-01-25 15:24:48 +01:00
Mădălin Ionel Patrașcu
718223c58c
gnu: Add python-phylophlan.
* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-01-25 00:22:53 +01:00
Mădălin Ionel Patrașcu
ed56d2a1c2
gnu: Add python-hclust2.
* gnu/packages/bioinformatics.scm (python-hclust2): New variable.
2023-01-25 00:22:53 +01:00
Mădălin Ionel Patrașcu
47839a9ed6
gnu: Add python-cmseq.
* gnu/packages/bioinformatics.scm (python-cmseq): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-01-25 00:22:53 +01:00
Ricardo Wurmus
9558da5bb4
gnu: Add python-bcbio-gff/biopython-1.73.
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable.
2023-01-25 00:22:53 +01:00
Navid Afkhami
43b7a033e3
gnu: Add r-tsis.
* gnu/packages/bioinformatics.scm (r-tsis): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-01-20 11:06:43 +01:00
Navid Afkhami
ddfe68ebbe
gnu: Add r-doubletcollection.
* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-01-20 11:02:37 +01:00
Simon Tournier
a7f1a1c0f0
gnu: Add python-vireosnp.
* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
2023-01-20 10:40:59 +01:00
Tobias Geerinckx-Rice
ae071e21f3
gnu: gdcm: Fix recursive Git source hash.
The hash being used covered only the gdcm repository, not the gdcmdata
submodule.

* gnu/packages/bioinformatics.scm (gdcm)[source]: Update hash.

Reported by civodul in #guix.
2023-01-15 01:00:00 +01:00
Tor-björn Claesson
2bdbd962e3
gnu: gdcm: Update to 3.0.20.
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20.
[home-page, license]: Update.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-17 16:05:20 +01:00
Ricardo Wurmus
bdcdab3676
gnu: r-cytonorm: Update to 0.0.10-1.166f9ff.
* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
2023-01-16 23:54:20 +01:00
Ricardo Wurmus
9ad5c3deea
gnu: r-signac: Update to 1.9.0-1.af41427.
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.9.0-1.af41427.
[propagated-inputs]: Remove r-ggforce, r-ggrepel, r-ggseqlogo, r-lsa,
r-qlcmatrix, and r-seurat; add r-vctrs.
2023-01-13 10:51:23 +01:00
Marius Bakke
7f7907335d
gnu: python-cellbender: Update source hash.
The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52
to d92cfc5a55c8b1771348468035993c52df975170.

* gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
2023-01-13 03:19:40 +01:00
Simon Tournier
483bc044eb
gnu: Add cellsnp-lite.
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
2023-01-12 21:37:56 +01:00
Ricardo Wurmus
de48bcee07
gnu: Add r-gg3d.
* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
2023-01-09 14:50:26 +01:00
Ricardo Wurmus
a4d9ce5488
gnu: Move Java XML packages to new module.
* gnu/packages/xml.scm (java-simple-xml, java-jaxp,
java-apache-xml-commons-resolver, java-jaxen, java-xom, java-xsdlib,
java-xpp3, java-xmlpull2, java-xmlpull-api-v1, java-dom4j, java-kxml2,
java-stax, java-jettison, java-jdom2, java-xstream, java-mxparser): Move these
variables from here...
* gnu/packages/java-xml.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register new file.
* gnu/packages/axoloti.scm,
gnu/packages/batik.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/groovy.scm,
gnu/packages/java.scm,
gnu/packages/maven.scm: Adjust module imports.
2023-01-08 23:20:59 +01:00
Antero Mejr
15caeb745c
gnu: Add gdcm.
* gnu/packages/bioinformatics.scm (gdcm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-08 16:11:45 +01:00
Marius Bakke
edbacab995
gnu: Use old setuptools in packages that relies on use_2to3 conversion.
This fixes a regression since 520cdf8058 where
the use_2to3 functionality was removed from setuptools.

* gnu/packages/graph.scm (python-louvain)[native-inputs]: Change from
PYTHON-SETUPTOOLS to PYTHON-SETUPTOOLS-57.
* gnu/packages/python-check.scm (python-parameterizedtestcase)[native-inputs]:
Likewise.
* gnu/packages/python-xyz.scm (python-anyjson)[native-inputs]: Add
PYTHON-SETUPTOOLS-57.
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Change from
PYTHON-SETUPTOOLS-FOR-TENSORFLOW to PYTHON-SETUPTOOLS-57.
2023-01-07 21:04:26 +01:00
Ricardo Wurmus
1dd8359fa2
gnu: bbmap: Update to 39.01.
* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
2023-01-06 15:12:07 +01:00
Ricardo Wurmus
f72dc615ab
gnu: bbmap: Use gexp.
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
2023-01-06 15:11:48 +01:00
Ricardo Wurmus
04ea0e7de4
gnu: nanopolish: Drop input labels.
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
2023-01-06 15:01:05 +01:00
Ricardo Wurmus
24e5dbb57a
gnu: nanopolish: Update to 0.14.0.
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0.
[source]: Update snippet.
[arguments]: Use gexp; use cc-for-target; drop #T from build phases.
[inputs]: Add minimap2.
[native-inputs]: Add cmake-minimal.
2023-01-06 14:51:55 +01:00