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2023-02-19gnu: 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. Tobias Geerinckx-Rice
2023-02-16gnu: 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. Efraim Flashner
2023-02-16gnu: 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. Ricardo Wurmus
2023-02-13gnu: jellyfish: Remove confusing quoting syntax....* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Do not mix quasiquote with gexp. Ricardo Wurmus
2023-02-13gnu: jellyfish: Drop input labels....* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Drop package labels. Ricardo Wurmus
2023-02-13gnu: fastp: Update to 0.23.2....* gnu/packages/bioinformatics.scm (fastp): Update to 0.23.2. [inputs]: Remove zlib; add isa-l and libdeflate. Ricardo Wurmus
2023-02-13gnu: fastp: Simplify....* gnu/packages/bioinformatics.scm (fastp)[arguments]: Simplify gexp. Ricardo Wurmus
2023-02-13gnu: fastqc: Use gexp....* gnu/packages/bioinformatics.scm (fastqc)[arguments]: Use gexp; drop trailing #T from build phase. [inputs]: Drop package labels. Ricardo Wurmus
2023-02-11gnu: 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. Efraim Flashner
2023-02-10gnu: 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. Ricardo Wurmus
2023-02-10gnu: Add python-doubletdetection....* gnu/packages/bioinformatics.scm (python-doubletdetection): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de> Ricardo Wurmus
2023-02-10gnu: Add python-phenograph....* gnu/packages/bioinformatics.scm (python-phenograph): New variable. Ricardo Wurmus
2023-02-10gnu: Add louvain....* gnu/packages/bioinformatics.scm (louvain): New variable. Ricardo Wurmus
2023-02-09gnu: Add python-scrublet....* gnu/packages/bioinformatics.scm (python-scrublet): New variable. Navid Afkhami
2023-02-07gnu: Add bitmapperbs....* gnu/packages/bioinformatics.scm (bitmapperbs): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-02-07Revert "gnu: Add bitmapperbs."...This reverts commit f55cc9cb0fb6c5dd56196009681e042c1aef415d. This commit was prematurely pushed. Ricardo Wurmus
2023-02-07gnu: Add bitmapperbs....* gnu/packages/bioinformatics.scm (bitmapperbs): New variable. Navid Afkhami
2023-02-06gnu: Add r-ggsankey....* gnu/packages/bioinformatics.scm (r-ggsankey): New variable. Ricardo Wurmus
2023-02-03gnu: Add r-psupertime....* gnu/packages/bioinformatics.scm (r-psupertime): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-02-03gnu: Add python-demuxem....* gnu/packages/bioinformatics.scm (python-demuxem): New variable. Navid Afkhami
2023-02-03gnu: Add python-pegasusio....* gnu/packages/bioinformatics.scm (python-pegasusio): New variable. Navid Afkhami
2023-02-03gnu: Add r-streamgraph....* gnu/packages/bioinformatics.scm (r-streamgraph): New variable. Navid Afkhami
2023-01-25gnu: 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> Tor-björn Claesson
2023-01-25gnu: gdcm: Ignore 3 failing tests....* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more failing tests. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Tor-björn Claesson
2023-01-25gnu: Add python-slamdunk....* gnu/packages/bioinformatics.scm (python-slamdunk): New variable. Ricardo Wurmus
2023-01-25gnu: Add python-phylophlan....* gnu/packages/bioinformatics.scm (python-phylophlan): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>. Mădălin Ionel Patrașcu
2023-01-25gnu: Add python-hclust2....* gnu/packages/bioinformatics.scm (python-hclust2): New variable. Mădălin Ionel Patrașcu
2023-01-25gnu: Add python-cmseq....* gnu/packages/bioinformatics.scm (python-cmseq): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>. Mădălin Ionel Patrașcu
2023-01-25gnu: Add python-bcbio-gff/biopython-1.73....* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable. Ricardo Wurmus
2023-01-20gnu: Add r-tsis....* gnu/packages/bioinformatics.scm (r-tsis): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-01-20gnu: Add r-doubletcollection....* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-01-20gnu: Add python-vireosnp....* gnu/packages/bioinformatics.scm (python-vireosnp): New variable. Simon Tournier
2023-01-15gnu: 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. Tobias Geerinckx-Rice
2023-01-17gnu: 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> Tor-björn Claesson
2023-01-16gnu: r-cytonorm: Update to 0.0.10-1.166f9ff....* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff. Ricardo Wurmus
2023-01-13gnu: 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. Ricardo Wurmus
2023-01-13gnu: 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. Marius Bakke
2023-01-12gnu: Add cellsnp-lite....* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable. Simon Tournier
2023-01-09gnu: Add r-gg3d....* gnu/packages/bioinformatics.scm (r-gg3d): New variable. Ricardo Wurmus
2023-01-08gnu: 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. Ricardo Wurmus
2023-01-08gnu: Add gdcm....* gnu/packages/bioinformatics.scm (gdcm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Antero Mejr
2023-01-07gnu: Use old setuptools in packages that relies on use_2to3 conversion....This fixes a regression since 520cdf80581669646ff61e9f18f3b27045556e76 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. Marius Bakke
2023-01-06gnu: bbmap: Update to 39.01....* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01. Ricardo Wurmus
2023-01-06gnu: bbmap: Use gexp....* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp. Ricardo Wurmus
2023-01-06gnu: nanopolish: Drop input labels....* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels. Ricardo Wurmus
2023-01-06gnu: 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. Ricardo Wurmus
2023-01-06gnu: filtlong: Use Python 3....* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with python-wrapper. Ricardo Wurmus
2023-01-06gnu: filtlong: Use gexp....* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp. Ricardo Wurmus
2023-01-06gnu: filtlong: Drop input labels....* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels. Ricardo Wurmus
2023-01-06gnu: filtlong: Remove trailing #T from build phases....* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T. Ricardo Wurmus