Navid Afkhami
9aad3dfd7b
gnu: Add r-tictoc.
...
* gnu/packages/bioinformatics.scm (r-tictoc): New variable.
2023-03-03 15:11:43 +01:00
Navid Afkhami
573b65f51e
gnu: Add r-ggexpress.
...
* gnu/packages/bioinformatics.scm (r-ggexpress): New variable.
2023-03-03 15:11:43 +01:00
Navid Afkhami
fd099793c8
gnu: Add r-markdownreports.
...
* gnu/packages/bioinformatics.scm (r-markdownreports): New variable.
2023-03-03 15:11:43 +01:00
Navid Afkhami
8eb8af7e30
gnu: Add r-markdownhelpers.
...
* gnu/packages/bioinformatics.scm (r-markdownhelpers): New variable.
2023-03-03 15:11:43 +01:00
Navid Afkhami
ba47b0fceb
gnu: Add r-codeandroll2.
...
* gnu/packages/bioinformatics.scm (r-codeandroll2): New variable.
2023-03-03 15:11:43 +01:00
Navid Afkhami
877e2e7cf3
gnu: Add r-readwriter.
...
* gnu/packages/bioinformatics.scm (r-readwriter): New variable.
2023-03-03 15:11:43 +01:00
Navid Afkhami
351de7426c
gnu: Add r-stringendo.
...
* gnu/packages/bioinformatics.scm (r-stringendo): New variable.
2023-03-03 15:11:42 +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
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
Efraim Flashner
7b58f14445
gnu: texlive-fancyvrb: Use over deprecated texlive-latex-fancyvrb.
...
* gnu/packages/bioinformatics.scm (phyml)[native-inputs],
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Replace
texlive-latex-fancyvrb with texlive-fancyvrb.
2023-01-30 20:07:50 +02:00
Efraim Flashner
bd3e3d87a9
gnu: texlive-graphics: Use over deprecated texlive-latex-graphics.
...
* gnu/packages/bioinformatics.scm (phyml)[native-inputs],
* gnu/packages/chemistry.scm (yaehmop)[native-inputs],
* gnu/packages/graphviz.scm (dot2tex)[propagated-inputs],
* gnu/packages/maths.scm (cddlib)[native-inputs],
* gnu/packages/statistics.scm (r-with-tests)[native-inputs],
* gnu/packages/tex.scm (texlive-apa6)[propagated-inputs]: Replace
texlive-latex-graphics with texlive-graphics.
2023-01-30 20:07:49 +02:00
Efraim Flashner
4cf1acc7f3
Merge remote-tracking branch 'origin/master' into core-updates
...
Conflicts:
doc/guix.texi
gnu/local.mk
gnu/packages/admin.scm
gnu/packages/base.scm
gnu/packages/chromium.scm
gnu/packages/compression.scm
gnu/packages/databases.scm
gnu/packages/diffoscope.scm
gnu/packages/freedesktop.scm
gnu/packages/gnome.scm
gnu/packages/gnupg.scm
gnu/packages/guile.scm
gnu/packages/inkscape.scm
gnu/packages/llvm.scm
gnu/packages/openldap.scm
gnu/packages/pciutils.scm
gnu/packages/ruby.scm
gnu/packages/samba.scm
gnu/packages/sqlite.scm
gnu/packages/statistics.scm
gnu/packages/syndication.scm
gnu/packages/tex.scm
gnu/packages/tls.scm
gnu/packages/version-control.scm
gnu/packages/xml.scm
guix/build-system/copy.scm
guix/scripts/home.scm
2023-01-30 12:39:40 +02:00
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
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
Ricardo Wurmus
8ace894681
gnu: filtlong: Use Python 3.
...
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with
python-wrapper.
2023-01-06 14:06:13 +01:00
Ricardo Wurmus
067c8a7445
gnu: filtlong: Use gexp.
...
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
2023-01-06 14:05:58 +01:00
Ricardo Wurmus
0070e52ade
gnu: filtlong: Drop input labels.
...
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
2023-01-06 13:59:04 +01:00
Ricardo Wurmus
f5ffcd31c2
gnu: filtlong: Remove trailing #T from build phases.
...
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
2023-01-06 13:58:05 +01:00
Ricardo Wurmus
e20ca244db
gnu: ngless: Use gexp.
...
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
2023-01-06 13:56:34 +01:00
Ricardo Wurmus
648c370f33
gnu: ngless: Remove trailing #T from build phases.
...
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Remove trailing #T.
2023-01-06 13:45:06 +01:00
Ricardo Wurmus
ec5b9fe27e
gnu: bamtools: Build shared libraries.
...
* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared
libraries instead of static libs.
2023-01-04 19:49:59 +01:00
Ricardo Wurmus
10e1025c63
gnu: Add scallop.
...
* gnu/packages/bioinformatics.scm (scallop): New variable.
2023-01-04 17:14:01 +01:00
Ricardo Wurmus
cad1789b3e
gnu: Add python-bcbio-gff.
...
* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
2023-01-03 15:43:25 +01:00
Ricardo Wurmus
e84f17ea93
gnu: Add r-domultibarheatmap.
...
* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
2022-12-30 15:06:12 +01:00
Ricardo Wurmus
bbada5967d
gnu: r-giotto: Update to 1.1.2-1.3c8067c.
...
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c.
2022-12-28 19:26:10 +01:00
Ricardo Wurmus
d8a9d55b57
gnu: Add r-bedtorch.
...
* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
2022-12-22 11:18:02 +01:00
Ricardo Wurmus
6d2f312b23
gnu: Add r-rhtslib12.
...
* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable.
2022-12-22 11:17:52 +01:00
Ricardo Wurmus
2a4930a1e6
gnu: Add wiggletools.
...
* gnu/packages/bioinformatics.scm (wiggletools): New variable.
2022-12-22 10:29:20 +01:00
Navid Afkhami
87c3fab854
gnu: Add python-episcanpy.
...
* gnu/packages/bioinformatics.scm (python-episcanpy): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-22 00:17:43 +01:00
Navid Afkhami
d07543b886
gnu: Add python-bamnostic.
...
* gnu/packages/bioinformatics.scm (python-bamnostic): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-22 00:14:05 +01:00
Ricardo Wurmus
9e495087d2
gnu: Add vembrane.
...
* gnu/packages/bioinformatics.scm (vembrane): New variable.
2022-12-21 23:12:41 +01:00
Ricardo Wurmus
1194cb1c40
gnu: python-plastid: Update to 0.6.0.
...
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.0.
[source]: Fetch from git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests; add build phases 'unpack-test-data and
'build-extensions.
[inputs]: Add openssl.
[native-inputs]: Add test data.
2022-12-21 23:12:40 +01:00
Ricardo Wurmus
bc4eac5d79
gnu: python-pysam: Update to 0.20.0.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.20.0.
[build-system]: Use pyproject-build-system.
2022-12-21 23:12:40 +01:00
Ricardo Wurmus
50948b8c3d
gnu: htslib: Update to 1.16.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.16.
2022-12-21 23:12:40 +01:00
Ricardo Wurmus
e34639c262
gnu: pbbam: Use htslib 1.14.
...
* gnu/packages/bioinformatics.scm (pbbam)[propagated-inputs]: Replace htslib
with htslib-1.14.
2022-12-21 23:12:40 +01:00
Ricardo Wurmus
5ccc017389
gnu: Add htslib-1.14.
...
* gnu/packages/bioinformatics.scm (htslib-1.14): New variable.
2022-12-21 23:12:40 +01:00
Ricardo Wurmus
9cb42f725a
gnu: python-scanpy: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'build and 'install phases; move pytest arguments
to #:test-flags; add 'pretend-version phase; replace custom 'check phase with
'delete-bad-tests phase.
2022-12-18 15:46:18 +01:00
Ricardo Wurmus
6aebf864a7
gnu: python-multivelo: Simplify with pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'build and 'install phases.
2022-12-18 15:46:18 +01:00
Ricardo Wurmus
1689215a30
gnu: bedtools-2.18: Use gexp.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp.
[native-inputs]: Drop package label.
2022-12-14 22:47:43 +01:00
Ricardo Wurmus
3d2b2f12e5
gnu: bedops: Update to 2.4.41.
...
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41.
[arguments]: Remove trailing #T from build phases; do not set BINDIR in
make-flags; set CC; replace 'install phase.
[native-inputs]: Add diffutils, perl, and which.
2022-12-13 18:22:55 +01:00
Ricardo Wurmus
23322c2de8
gnu: tophat: Remove trailing #T from build phases and snippet.
...
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from
snippet.
[arguments]: Remove trailing #T from build phases.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
b339e181e1
gnu: python-bx-python: Update to 0.9.0.
...
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'build-extensions and 'disable-cython-doctests.
[native-inputs]: Replace python-nose with python-pytest.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
de30c74b63
gnu: bioawk: Use gexp.
...
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify
'install phase.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
057579495f
gnu: blasr-libcpp: Remove trailing #T from build phases.
...
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove
trailing #T from build phases.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
eaf5198a5e
gnu: pbbam: Drop input labels.
...
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
8b2fdcb2c3
gnu: pbbam: Update to 2.1.0.
...
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
684d046e6c
gnu: pbcopper: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
2022-12-13 16:31:55 +01:00
Ricardo Wurmus
53f65f7315
gnu: bedtools: Remove unnecessary quasiquotation.
...
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote.
[native-inputs]: Drop input label.
2022-12-13 16:31:54 +01:00
Ricardo Wurmus
4f1a36bd7b
gnu: bamutils: Update to 1.0.15.
...
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15.
[arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags.
[native-inputs]: Update libstatgen.
2022-12-13 16:31:54 +01:00
Ricardo Wurmus
8cc22866c2
gnu: bamtools: Update to 2.5.2.
...
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2.
[arguments]: Enable tests; remove extra phases.
[inputs]: Add jsoncpp.
[native-inputs]: Add pkg-config.
2022-12-13 16:31:54 +01:00
Ricardo Wurmus
6d2afaf25b
gnu: aragorn: Update to 1.2.41.
...
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41.
[source]: Fetch C source file from new location.
[arguments]: Drop trailing #T in build phases; use gexp.
[native-inputs]: Add origin for man page.
[home-page]: Update to new home page.
[license]: Update to GPLv3+.
2022-12-13 16:31:54 +01:00
Ricardo Wurmus
e84042fdd4
gnu: cnvkit: Update to 0.9.9.
...
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
2022-12-13 00:08:54 +01:00
Ricardo Wurmus
1369b53d49
gnu: seqmagick: Update to 0.8.4.
...
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
2022-12-13 00:08:54 +01:00
Ricardo Wurmus
461dff2651
gnu: python-cgatcore: Update to 0.6.14.
...
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
2022-12-13 00:08:54 +01:00
Ricardo Wurmus
b72df3bbb3
gnu: python-dna-features-viewer: Update to 3.1.1.
...
* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
2022-12-13 00:07:23 +01:00
Ricardo Wurmus
b66b6bdf70
gnu: python-hicexplorer: Update to 3.7.2.
...
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
2022-12-13 00:07:23 +01:00
Ricardo Wurmus
c3e330cf36
gnu: python-pygenometracks: Update to 3.5.
...
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
2022-12-13 00:07:22 +01:00
Ricardo Wurmus
6e9518e201
gnu: python-hicmatrix: Update to 16.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
2022-12-13 00:07:22 +01:00
Ricardo Wurmus
5167881a60
gnu: python-biopython: Update to 1.80.
...
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
2022-12-13 00:07:22 +01:00
Ricardo Wurmus
2c8a53cb6b
gnu: bioperl-minimal: Remove trailing #T from build phase.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal)[arguments]: Remove
trailing #T from build phase.
2022-12-12 14:37:03 +01:00
Ricardo Wurmus
fd44d489b5
gnu: python-biom-format: Update to 2.1.12.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12.
[arguments]: Remove "relax" phase; update "disable-broken-tests" phase.
[propagated-inputs]: Add python-scikit-bio.
2022-12-02 21:46:36 +01:00
Ricardo Wurmus
b93e21a213
gnu: Add python-scikit-bio.
...
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
2022-12-02 21:46:36 +01:00
Ricardo Wurmus
62da3f9837
gnu: python-pairtools: Update to 1.0.2.
...
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2.
[source]: Update Github URL.
[arguments]: Update patch in "fix-references" phase.
[native-inputs]: Remove python-nose.
[inputs]: Remove.
[propagated-inputs]: Add python-bioframe, python-pandas, python-pysam,
python-pyyaml, and python-scipy.
[home-page]: Update.
2022-12-02 21:46:36 +01:00
Ricardo Wurmus
089b2e4f65
gnu: python-pairtools: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests
conditionally.
2022-12-02 21:46:36 +01:00
Ricardo Wurmus
631ea9a411
gnu: python-pybedtools: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use
pyproject-build-system.
[arguments]: Import (guix build pyproject-build-system).
2022-12-02 21:46:36 +01:00
Ricardo Wurmus
a268b1ba91
gnu: python-htsget: Update to 0.2.6.
...
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6.
[build-system]: Use pyproject-build-system.
2022-12-02 21:46:35 +01:00
Ricardo Wurmus
16ecce39d2
gnu: python-cellbender: Update to 0.2.2.
...
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2.
[build-system]: Use pyproject-build-system.
2022-12-02 21:46:35 +01:00
Ricardo Wurmus
62ddd3bc80
gnu: Add python-fanc.
...
* gnu/packages/bioinformatics.scm (python-fanc): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02 17:43:20 +01:00
Ricardo Wurmus
ee069ec651
gnu: Add python-genomic-regions.
...
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02 17:20:54 +01:00
Navid Afkhami
b095dac8e0
gnu: Add r-btools.
...
* gnu/packages/bioinformatics.scm (r-btools): New variable.
2022-11-25 11:17:56 +01:00
Ricardo Wurmus
ebde19092f
gnu: r-circus: Update to 0.1.7.
...
* gnu/packages/bioinformatics.scm (r-circus): Update to 0.1.7.
[properties]: Add upstream-name property.
[propagated-inputs]: Add r-biocgenerics, r-genomeinfodb, and r-rtracklayer.
2022-11-17 15:00:49 +01:00
Ricardo Wurmus
02db3f51b7
gnu: Add r-disgenet2r.
...
* gnu/packages/bioinformatics.scm (r-disgenet2r): New variable.
2022-11-15 11:03:24 +01:00
Mădălin Ionel Patrașcu
b4e3e02fd1
gnu: Add r-pando.
...
* gnu/packages/bioinformatics.scm (r-pando): New variable.
2022-11-09 09:55:14 +01:00
Mădălin Ionel Patrașcu
49e1a3a04b
gnu: Add python-cooltools.
...
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
2022-11-04 13:50:20 +01:00
Mădălin Ionel Patrașcu
14cbaac69c
gnu: Add python-bioframe.
...
X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
2022-11-04 13:39:12 +01:00
Ricardo Wurmus
1b0fea29a0
gnu: r-dyngen: Update to 1.0.5.
...
* gnu/packages/bioinformatics.scm (r-dyngen): Update to 1.0.5.
2022-11-04 10:01:05 +01:00
Vagrant Cascadian
15ff5eebb6
gnu: Fix various lint issues in synopsis and descriptions.
...
* gnu/packages/android.scm (etc1tool)[synopsis]: Drop trailing period.
* gnu/packages/bioinformatics.scm (mudskipper)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-async-log-attributes-1)[synopsis]: Likewise.
(rust-atomic-polyfill-1)[synopsis]: Likewise.
(rust-modifier-0.1)[synopsis]: Likewise.
(rust-openssl-macros-0.1)[synopsis]: Likewise.
(rust-syn-mid-0.5)[synopsis]: Likewise.
(rust-toml-edit-0.14)[synopsis]: Likewise.
(rust-valuable-derive-0.1)[synopsis]: Likewise.
(rust-inflections-1)[synopsis]: Likewise.
* gnu/packages/databases.scm (python-databases)[synopsis]: Likewise.
* gnu/packages/games.scm (liquidwar6)[synopsis]: Likewise.
* gnu/packages/golang.scm (go-golang.org-x-sync-errgroup)[synopsis]: Likewise.
* gnu/packages/guile-xyz.scm (guile-config)[synopsis]: Likewise.
* gnu/packages/haskell-web.scm (ghc-hxt-xpath)[synopsis]: Likewise.
* gnu/packages/haskell-xyz.scm (ghc-string-qq)[synopsis]: Likewise.
* gnu/packages/machine-learning.scm (python-lap)[synopsis]: Likewise.
(python-pyro-api)[synopsis]: Likewise.
* gnu/packages/messaging.scm (python-librecaptcha)[synopsis]: Likewise.
* gnu/packages/python-check.scm (python-pytest-cram)[synopsis]: Likewise.
* gnu/packages/python-web.scm (python-jschema-to-python)[synopsis]: Likewise.
(python-sarif-om)[synopsis]: Likewise.
(python-socksio)[synopsis]: Likewise.
(python-msrest)[synopsis]: Likewise.
* gnu/packages/tor.scm (torsocks)[synopsis]: Likewise.
* gnu/packages/cran.scm (r-rlist)[synopsis]: Remove leading article.
* gnu/packages/crates-io.scm (rust-clippy-lints-0.0.153)[synopsis]: Likewise.
(rust-simplelog-0.11)[synopsis]: Likewise.
* gnu/packages/samba.scm (wsdd)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-spki-0.4)[synopsis]: Remove trailing
whitespace.
* gnu/packages/golang.scm (go-github-com-mattn-go-zglob)[description]: Remove
leading whitespace.
* gnu/packages/haskell-check.scm (ghc-crypto-cipher-tests)[description]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-ctype)[synopsis]: Remove trailing
whitespace.
* gnu/packages/mpi.scm (openmpi-thread-multiple)[description]: Remove leading
whitespace.
* gnu/packages/node-xyz.scm (node-string-decoder)[synopsis]: Remove trailing
whitespace.
2022-10-31 18:13:48 -07:00
Ricardo Wurmus
75b24abf09
gnu: flair: Update to 1.6.4.
...
* gnu/packages/bioinformatics.scm (flair): Update to 1.6.4.
[propagated-inputs]: Add python-numpy and python-scipy.
2022-10-28 15:00:21 +02:00
Ricardo Wurmus
bb4f24b3ae
gnu: flair: Set R_HOME.
...
* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
2022-10-28 15:00:21 +02:00
Ricardo Wurmus
28950ed561
gnu: flair: Add missing R package.
...
* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
2022-10-28 15:00:20 +02:00
Ricardo Wurmus
176a501360
gnu: flair: Add missing R packages.
...
* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2.
[inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman,
and r-rlang.
[arguments]: Add phase "wrap-executable".
2022-10-27 18:21:22 +02:00
Mădălin Ionel Patrașcu
fe7b421d05
gnu: Add python-multivelo.
...
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
2022-10-27 15:15:19 +02:00
Hong.Li@mdc-berlin.de
358a1fdf7b
gnu: Add r-seuratwrappers.
...
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
2022-10-27 15:03:21 +02:00
Vagrant Cascadian
a2e4e3489b
gnu: Various typo fixes.
...
* gnu/packages/emacs-xyz.scm (emacs-popup-kill-ring)[description]: Fix very
sneaky "This packages" variant. Thanks to nckhexen!
* gnu/packages/bioinformatics.scm (r-icellnet)[description]: Fix use of
"allows to".
* gnu/packages/check.scm (python-pytest-freezegun)[description]: Ditto.
* gnu/packages/linux.scm (tp-smapi-module)[description]: Ditto.
* gnu/packages/mail.scm (procmail): Ditto.
* gnu/packages/maths.scm (maxima): Ditto.
* gnu/packages/samba.scm (wsdd)[description]: Ditto.
* gnu/packages/ssh.scm (openssh): Ditto.
2022-10-24 17:35:19 -07:00
Vagrant Cascadian
d3e982dccb
gnu: Fix typos.
...
* gnu/packages/emacs-xyz.scm (emacs-piem)[description]: Fix use of "This
packages".
* gnu/packages/tex.scm (texlive-hardwrap)[description]: Fix spelling of
"arbitrary".
* gnu/packages/cran.scm (r-shinymanager)[description]: Fix spelling of
"authentication".
* gnu/packages/lisp-xyz.scm (sbcl-utils-kt)[description]: Fix spelling of
"developed".
* gnu/packages/crates-io.scm (rust-fs-utils-1)[description]: Fix spelling of
"filesystem".
[synopsis]: Likewise.
* gnu/packages/haxe.scm (neko)[description]: Fix spelling of "functions".
* gnu/packages/animation.scm (swftools)[description]: Fix needless
pluralization of "information".
* gnu/packages/lisp-xyz.scm (sbcl-slot-extra-options)[description]: Fix
spelling of "inheritance".
* gnu/packages/emacs-xyz.scm (emacs-js-comint)[description]: Fix spelling of
"interpreter".
* gnu/packages/coq.scm (coq-mathcomp-finmap)[description]: Fix spelling of
"library".
* gnu/services/lightdm.scm (lightdm-configuration): Fix spelling of
"mechanism".
* gnu/packages/emacs-xyz.scm (emacs-citar-org-roam)[synopsis]: Fix spelling of
"package".
* gnu/packages/games.scm (freerct)[description]: Fix spelling of
"responsibilities".
* gnu/packages/statistics.scm (r-mixedpower)[description]: Fix spelling of
"separate".
* gnu/packages/accessibility.scm (espeakup)[description]: Fix spelling of
"speech".
* gnu/packages/bioinformatics.scm (r-skitools)[synopsis]: Fix spelling of
"utilities".
* gnu/packages/golang.scm (go-github-com-savsgio-gotils)[synopsis]: Fix
spelling of "utilities".
[description]: Likewise.
* gnu/system.scm (boot-file-system-service os): Fix spelling of "utilities".
2022-10-23 17:03:09 -07:00
Ricardo Wurmus
f24b66bf4a
gnu: pigx-sars-cov-2: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.8.
[arguments]: Add build phase 'unpack-databases; enable tests.
[native-inputs]: Add origins for databases; remove automake and autoconf.
[inputs]: Add r-data-table, r-deconvr, r-htmltools, r-jsonlite, r-knitr, and
r-mass.
2022-10-08 12:06:41 +02:00
Christopher Baines
020dc0a1f1
gnu: plink: Change origin URL.
...
pngu.mgh.harvard.edu seems to time out.
* gnu/packages/bioinformatics.scm (plink)[origin]. Change URL.
2022-10-06 15:08:02 +01:00
Ricardo Wurmus
fd6cd9de86
gnu: Add megahit.
...
* gnu/packages/bioinformatics.scm (megahit): New variable.
2022-10-05 17:59:04 +02:00
Ricardo Wurmus
be1d561f1a
gnu: Add cd-hit-auxtools.
...
* gnu/packages/bioinformatics.scm (cd-hit-auxtools): New variable.
2022-10-05 14:28:24 +02:00
Ricardo Wurmus
3f627bf56b
gnu: cd-hit: Update to 4.8.1.
...
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.8.1.
[arguments]: Do not use quasiquote; remove trailing #T from build phases.
[inputs]: Add zlib.
2022-10-05 13:47:57 +02:00
Ricardo Wurmus
9ed65e6af7
gnu: kaiju: Update to 1.9.0.
...
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0.
[arguments]: Use gexps; wrap scripts in install phase.
[inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip,
python-wrapper, tar, and wget.
2022-10-04 23:10:56 +02:00
Ricardo Wurmus
1266b9ed11
gnu: salmon: Update to 1.9.0.
...
* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0.
[arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish
itlib headers.
[inputs]: Use new label-less list; move pufferfish origin from here...
[native-inputs]: ...to here.
2022-09-30 22:43:21 +02:00
Ricardo Wurmus
729ce5fcf8
gnu: Add centrifuge.
...
* gnu/packages/bioinformatics.scm (centrifuge): New variable.
2022-09-30 16:59:18 +02:00
Ricardo Wurmus
1ee2d117d8
gnu: blast+: Build reproducibly.
...
Fixes <https://issues.guix.gnu.org/42141 >.
* gnu/packages/bioinformatics.scm (blast+)[source]: Do not record kernel
version and use fix set of random numbers.
2022-09-29 23:21:16 +02:00
Maxim Cournoyer
990a4822f1
Merge branch 'staging' into core-updates
...
Conflicts resolved in:
gnu/local.mk
gnu/packages/cran.scm
gnu/packages/gnome.scm
gnu/packages/gtk.scm
gnu/packages/icu4c.scm
gnu/packages/java.scm
gnu/packages/machine-learning.scm
gnu/packages/tex.scm
2022-09-27 15:59:30 -04:00
Ricardo Wurmus
c1716ab6ec
gnu: Add r-compgenomrdata.
...
* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
2022-09-26 17:21:57 +02:00
Ricardo Wurmus
cbe8391d7c
gnu: Add mudskipper.
...
* gnu/packages/bioinformatics.scm (mudskipper): New variable.
2022-09-23 00:21:40 +02:00
Ricardo Wurmus
1a1ff7ed8f
gnu: python-cooler: Skip broken test.
...
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add another
patch for tests/test_util.py.
2022-09-21 22:19:33 +02:00
Ricardo Wurmus
cd5bbb9b42
gnu: python-cooler: Do not use flake8.
...
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add build phase
'do-not-use-flake8.
2022-09-21 22:19:33 +02:00
Ricardo Wurmus
d871080a41
gnu: Add r-chromunity.
...
* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
2022-09-21 11:09:46 +02:00
Ricardo Wurmus
a7f6392caa
gnu: Add r-skitools.
...
* gnu/packages/bioinformatics.scm (r-skitools): New variable.
2022-09-21 11:09:46 +02:00
Ricardo Wurmus
af663c9e48
gnu: Add r-gchain.
...
* gnu/packages/bioinformatics.scm (r-gchain): New variable.
2022-09-21 11:09:46 +02:00
Ricardo Wurmus
6ad4d74aca
gnu: Add r-gtrack.
...
* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
2022-09-21 11:09:46 +02:00
Ricardo Wurmus
29634a4ce3
gnu: Add r-bamutils.
...
* gnu/packages/bioinformatics.scm (r-bamutils): New variable.
2022-09-21 11:09:45 +02:00
Ricardo Wurmus
4bd64dde2b
gnu: Add r-gutils.
...
* gnu/packages/bioinformatics.scm (r-gutils): New variable.
2022-09-21 11:09:41 +02:00
Ricardo Wurmus
8084e3bdb3
gnu: python-pyvcf: Update to 0.6.8-0.476169c.
...
* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
2022-09-20 17:02:34 +02:00
