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Author SHA1 Message Date
Mathieu Othacehe a1eca979fb
Merge remote-tracking branch 'origin/master' into core-updates-frozen. 2021-10-12 17:46:23 +00:00
Felix Gruber 9101c7bf8e
gnu: clipper: Disable non-deterministic test. 
This test fails/succeeds non-deterministically.

* gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable
  non-deterministic test test_get_FDR_cutoff_mean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-10-12 18:13:29 +02:00
Lars-Dominik Braun c8a7ba621b
gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:55 +02:00
Lars-Dominik Braun 26488f63b8
gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:55 +02:00
Lars-Dominik Braun 07f2e4993b
gnu: pigx-chipseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun e51a3f4a72
gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun fb1ffc53ba
gnu: pigx-bsseq: Remove dependency on pandoc-citeproc. 
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun 7eb9fe4e53
gnu: ngless: Fix build. 
Apply upstream patch to restore compatibility with current Stackage.

* gnu/packages/patches/ngless-unliftio.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bioinformatics.scm (ngless): Use it.
 2021-10-08 09:13:53 +02:00
Lars-Dominik Braun b97f549b14
gnu: Update Haskell ecosystem. 
Bump packages’ versions to the lastest Stackage or Hackage
release. Since packages are interdependent, do so in a single commit.

525 packages have been updated.

These packages have been removed, because they fail to build, have no
newer version available and no dependencies:

corrode
ghc-easytest
ghc-edisonapi
ghc-edisoncore
ghc-pandoc-types
ghc-regex-tdfa-text

These have been removed, because they are no longer required:

ghc-happy-1.19.9
ghc-prettyprinter-1.6
ghc-protolude-0.3

ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc
does not use them any more.

Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
 2021-10-08 09:13:52 +02:00
Ricardo Wurmus 53611ab5c5
gnu: pigx-chipseq: Update to 0.0.53. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
 2021-09-29 09:58:45 +02:00
Charles f36b789f78
gnu: Update some packages using old JavaScript minifier. 
* gnu/packages/minetest.scm (minetest-basic-trains): New variable.
* gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input.
* gnu/packages/ci.scm (laminar): Update uglifyjs input.
* gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker
r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input.
* gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-09-22 16:03:19 +03:00
zimoun f80824fe09
gnu: Add r-presto. 
* gnu/packages/bioinformatics.scm (r-presto): New variable.
 2021-09-20 17:23:16 +02:00
Ricardo Wurmus 0406f1c2e1
gnu: discrover: Update package name in texlive-union. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
 2021-09-13 22:49:56 +02:00
Ludovic Courtès d9dfbf886d
Merge branch 'master' into core-updates-frozen 2021-09-07 14:19:08 +02:00
Ludovic Courtès b949f34f31
gnu: Use the non-deprecated TeX packages. 
This commit leaves 'dblatex' and 'texlive-hyperref' as users of
deprecated packages, but these have many dependents.

* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use
non-deprecated TeX Live packages.
(velvet)[native-inputs]: Likewise.
* gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise.
(chez-web)[native-inputs]: Likewise.
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise.
* gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise.
* gnu/packages/maths.scm (hypre)[native-inputs]: Likewise.
* gnu/packages/music.scm (lilypond)[native-inputs]: Likewise.
* gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise.
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]:
Likewise.
(python-matplotlib-documentation)[native-inputs]: Likewise.
(python-ipython-documentation)[native-inputs]: Likewise.
(python-nbconvert)[native-inputs]: Likewise.
(python-pypandoc)[native-inputs]: Likewise.
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise.
* gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise.
(teximpatient)[native-inputs]: Likewise.
(texlive-latex-pgf)[propagated-inputs]: Likewise.
(texlive-beamer)[propagated-inputs]: Likewise.
 2021-09-06 22:02:15 +02:00
Ricardo Wurmus c82b723bf8
gnu: Add megadepth. 
* gnu/packages/bioinformatics.scm (megadepth): New variable.
 2021-09-06 14:48:24 +02:00
Felix Gruber 93bf42361c
gnu: Replace PYTHONPATH with GUIX_PYTHONPATH. 
In packages that do not use python-build-system, PYTHONPATH is generally
not defined. Instead we can use GUIX_PYTHONPATH which should contain all
Python dependencies.

* gnu/packages/bioinformatics.scm (shorah)[arguments]: Replace
  PYTHONPATH with GUIX_PYTHONPATH.
* gnu/packages/debug.scm (c-vise)[arguments]: Idem.
* gnu/packages/gnome.scm (drawing, apostrophe, ocrfeeder)[arguments]: Idem.
* gnu/packages/music.scm (a2jmidid)[arguments]: Idem.
* gnu/packages/syndication.scm (gfeeds)[arguments]: Idem.
* gnu/packages/xdisorg.scm (gammastep)[arguments]: Idem.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-09-06 10:47:54 +02:00
Ricardo Wurmus c75b30d58f
gnu: Add r-catch. 
* gnu/packages/bioinformatics.scm (r-catch): New variable.
 2021-09-01 14:53:36 +02:00
Ricardo Wurmus 4abf226833
gnu: Add scregseg. 
* gnu/packages/bioinformatics.scm (scregseg): New variable.
 2021-08-31 23:11:06 +02:00
Ricardo Wurmus a1ee212184
gnu: python-strawc: Propagate pybind11. 
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Ricardo Wurmus 55cb5a62a1
gnu: python-scanpy: Propagate sinfo. 
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Marius Bakke c4133c43c7
Merge branch 'master' into core-updates-frozen 
Conflicts:
	gnu/packages/algebra.scm
	gnu/packages/games.scm
	gnu/packages/golang.scm
	gnu/packages/kerberos.scm
	gnu/packages/mail.scm
	gnu/packages/python.scm
	gnu/packages/ruby.scm
	gnu/packages/scheme.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
 2021-08-12 00:30:27 +02:00
Marius Bakke b029be2ee0
Merge branch 'master' into core-updates-frozen 
Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/cmake.scm
	gnu/packages/curl.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/gpodder.scm
	gnu/packages/music.scm
	gnu/packages/patches/glibc-bootstrap-system.patch
	gnu/packages/python-xyz.scm
	gnu/packages/shells.scm
	gnu/packages/statistics.scm
 2021-07-29 22:34:57 +02:00
Ricardo Wurmus 7712154ccb
gnu: Add python-coolbox. 
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus b105655670
gnu: python-scanpy: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus d84ead8174
gnu: Add python-dna-features-viewer. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus e85b35070c
gnu: Add python-pybbi. 
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus db13eb962f
gnu: Add python-strawc. 
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus 17c765e2e1
gnu: Add r-cytonorm. 
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus f66759e0b2
gnu: Add ivar. 
* gnu/packages/bioinformatics.scm (ivar): New variable.
 2021-08-25 11:22:02 +02:00
Ricardo Wurmus 27952318a5
gnu: fastp: Update to 0.20.1. 
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
 2021-08-20 10:49:48 +02:00
Ricardo Wurmus 907f835e19
gnu: pigx-rnaseq: Update to 0.0.18. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
 2021-08-11 19:33:38 +02:00
Ricardo Wurmus a79ad5fce5
gnu: pigx-rnaseq: Update to 0.0.19. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
 2021-08-13 15:23:39 +02:00
Ricardo Wurmus f1b64c435a
gnu: pigx-sars-cov2-ww: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
 2021-08-05 16:46:34 +02:00
Ricardo Wurmus 2ab5d08fbe
gnu: Add r-spectre. 
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
 2021-08-03 10:43:08 +02:00
Ricardo Wurmus 3e5eff8c30
gnu: Add seqan 3. 
* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
 2021-07-26 11:54:21 +02:00
Ricardo Wurmus 99ca1ae4f8
gnu: Add segemehl. 
* gnu/packages/bioinformatics.scm (segemehl): New variable.
 2021-07-26 11:08:13 +02:00
Ludovic Courtès d468a03a00
gnu: Use 'search-input-directory' and 'search-input-file' where appropriate. 
This changes some of the remaining uses of this idiom:

  (string-append (assoc-ref inputs "LABEL") "FILE")

to one of:

  (search-input-file inputs "FILE")
  (search-input-directory inputs "FILE")

* gnu/packages/axoloti.scm (axoloti-patcher): Use
'search-input-directory'.
(axoloti-patcher-next): Likewise.
* gnu/packages/bioinformatics.scm (java-picard): Likewise.
* gnu/packages/bootloaders.scm (grub-hybrid): Likewise.
(u-boot-puma-rk3399): Likewise.
(u-boot-rock64-rk3328): Likewise.
(u-boot-firefly-rk3399): Likewise.
(u-boot-rockpro64-rk3399): Likewise.
(u-boot-pinebook-pro-rk3399): Likewise.
* gnu/packages/cran.scm (r-shiny): Likewise.
(r-shinytree): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Likewise.
(emacs-rime): Likewise.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/games.scm (bsd-games): Likewise.
(seahorse-adventures): Likewise.
(einstein): Likewise.
* gnu/packages/gimp.scm (gimp-fourier): Likewise.
* gnu/packages/gnome.scm (gspell): Likewise.
* gnu/packages/guile-xyz.scm (guile-libyaml): Likewise.
* gnu/packages/java.scm (icedtea-7): Likewise.
* gnu/packages/language.scm (nimf): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (claws-mail): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/scheme.scm (scm): Likewise.
* gnu/packages/security-token.scm (python-fido2): Likewise.
* gnu/packages/syndication.scm (rtv): Likewise.
* gnu/packages/tls.scm (acme-client): Likewise.
* gnu/packages/web.scm (netsurf): Likewise.
* gnu/packages/wine.scm (wine-staging): Likewise.
* gnu/packages/wxwidgets.scm (wxwidgets): Likewise.
 2021-07-24 16:23:24 +02:00
Ludovic Courtès 828cfdc47e
gnu: Use 'search-input-file' when looking for .jar files. 
* gnu/packages/bioinformatics.scm (java-picard-1.113): Use
'search-input-file' when looking for *.jar.
(fastqc): Likewise.
* gnu/packages/groovy.scm (groovy): Likewise.
* gnu/packages/java.scm (ant-bootstrap): Likewise.
(ecj-bootstrap): Likewise.
(java-cisd-base): Likewise.
(java-cisd-args4j): Likewise.
(java-cisd-jhdf5): Likewise.
(java-native-access): Likewise.
(java-native-access-platform): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès bc64d9554b
gnu: Use 'search-input-file' when looking for executables. 
* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when
looking for executables.
* gnu/packages/audio.scm (ableton-link): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (roary): Likewise.
(ngless): Likewise.
* gnu/packages/boost.scm (boost-for-irods): Likewise.
* gnu/packages/bootloaders.scm (grub): Likewise.
(grub-efi): Likewise.
* gnu/packages/chemistry.scm (inchi): Likewise.
* gnu/packages/dictionaries.scm (ding): Likewise.
* gnu/packages/dlang.scm (ldc): Likewise.
* gnu/packages/education.scm (childsplay): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise.
(emacs-haskell-mode): Likewise.
(emacs-auctex): Likewise.
(emacs-ggtags): Likewise.
(emacs-graphviz-dot-mode): Likewise.
(emacs-flycheck-grammalecte): Likewise.
(emacs-counsel-notmuch): Likewise.
(emacspeak): Likewise.
(emacs-exwm): Likewise.
(emacs-exwm-x): Likewise.
(emacs-treemacs): Likewise.
(emacs-telega): Likewise.
(emacs-exiftool): Likewise.
* gnu/packages/emulators.scm (higan): Likewise.
* gnu/packages/engineering.scm (freehdl): Likewise.
(librepcb): Likewise.
* gnu/packages/entr.scm (entr): Likewise.
* gnu/packages/file-systems.scm (libeatmydata): Likewise.
(xfstests): Likewise.
(mergerfs): Likewise.
(mergerfs-tools): Likewise.
* gnu/packages/finance.scm (monero-gui): Likewise.
* gnu/packages/flashing-tools.scm (flashrom): Likewise.
* gnu/packages/fontutils.scm (fontforge): Likewise.
* gnu/packages/game-development.scm (python2-renpy): Likewise.
* gnu/packages/games.scm (opensurge): Likewise.
(xboard): Likewise.
(hyperrogue): Likewise.
(flare-game): Likewise.
(chessx): Likewise.
* gnu/packages/geo.scm (grass): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/gnome.scm (mm-common): Likewise.
(network-manager-openvpn): Likewise.
(network-manager-vpnc): Likewise.
(network-manager-openconnect): Likewise.
(apostrophe): Likewise.
* gnu/packages/gnupg.scm (pius): Likewise.
(jetring): Likewise.
* gnu/packages/gnuzilla.scm (icedove): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
* gnu/packages/graphviz.scm (xdot): Likewise.
* gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise.
* gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise.
* gnu/packages/ibus.scm (ibus): Likewise.
* gnu/packages/image.scm (phockup): Likewise.
* gnu/packages/irc.scm (quassel): Likewise.
* gnu/packages/java.scm (drip): Likewise.
(ant-bootstrap): Likewise.
(tla2tools): Likewise.
* gnu/packages/julia.scm (julia): Likewise.
* gnu/packages/less.scm (lesspipe): Likewise.
* gnu/packages/libreoffice.scm (libreoffice): Likewise.
* gnu/packages/linux.scm (fuse): Likewise.
(lm-sensors): Likewise.
(bluez): Likewise.
(fakeroot): Likewise.
(inputattach): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise.
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise.
* gnu/packages/lua.scm (fennel): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (public-inbox): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
(maxima): Likewise.
(frama-c): Likewise.
* gnu/packages/messaging.scm (libgadu): Likewise.
* gnu/packages/music.scm (denemo): Likewise.
(curseradio): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
(squid): Likewise.
(aircrack-ng): Likewise.
* gnu/packages/node.scm (node): Likewise.
(node-llparse-frontend-bootstrap): Likewise.
(node-llparse-bootstrap): Likewise.
(llhttp-bootstrap): Likewise.
(node-lts): Likewise.
* gnu/packages/ocaml.scm (ocaml-4.11): Likewise.
(opam): Likewise.
(ocaml-graph): Likewise.
* gnu/packages/orpheus.scm (orpheus): Likewise.
* gnu/packages/password-utils.scm (password-store): Likewise.
* gnu/packages/python.scm (pypy3): Likewise.
* gnu/packages/qt.scm (qt5ct): Likewise.
* gnu/packages/radio.scm (libosmo-dsp): Likewise.
* gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise.
* gnu/packages/rust.scm (rust-1.30): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/suckless.scm (surf): Likewise.
* gnu/packages/syndication.scm (gfeeds): Likewise.
* gnu/packages/telephony.scm (mumble): Likewise.
* gnu/packages/terminals.scm (alacritty): Likewise.
* gnu/packages/tex.scm (texlive-bin): Likewise.
* gnu/packages/uml.scm (plantuml): Likewise.
* gnu/packages/version-control.scm (python-git-multimail): Likewise.
(gitolite): Likewise.
(hg-commitsigs): Likewise.
(git-when-merged): Likewise.
(git-imerge): Likewise.
(gita): Likewise.
* gnu/packages/video.scm (you-get): Likewise.
* gnu/packages/vim.scm (eovim): Likewise.
* gnu/packages/virtualization.scm (qemu): Likewise.
(virt-manager): Likewise.
(criu): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
(xl2tpd): Likewise.
* gnu/packages/wm.scm (i3lock-fancy): Likewise.
* gnu/packages/wxwidgets.scm (python-wxpython): Likewise.
(python2-wxpython): Likewise.
* gnu/packages/xdisorg.scm (autorandr): Likewise.
* gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise.
(v86d): Likewise.
(mkfontdir): Likewise.
(xpra): Likewise.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès 377e9453ca
gnu: Use 'search-input-file' when looking for *.so and *.a. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-file' when looking for *.a and *.so.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/engineering.scm (lepton-eda): Likewise.
(pcb): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/haskell.scm (ghc-7): Likewise.
* gnu/packages/irods.scm (irods): Likewise.
* gnu/packages/language.scm (python2-tegaki-pygtk): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-lzlib): Likewise.
(sbcl-cl-gobject-introspection): Likewise.
(sbcl-cl-ana): Likewise.
(sbcl-cl-libuv): Likewise.
(sbcl-cl-async): Likewise.
(sbcl-mcclim): Likewise.
(sbcl-zstd): Likewise.
(sbcl-cl-opengl): Likewise.
(sbcl-lev): Likewise.
(sbcl-cl-glfw3): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
* gnu/packages/messaging.scm (utox): Likewise.
* gnu/packages/mpi.scm (java-openmpi): Likewise.
* gnu/packages/music.scm (jack-select): Likewise.
* gnu/packages/pascal.scm (fpc): Likewise.
* gnu/packages/python-crypto.scm (python-libnacl): Likewise.
* gnu/packages/python-xyz.scm (python-cairocffi): Likewise.
(python-pyev): Likewise.
(python-pytidylib): Likewise.
* gnu/packages/radio.scm (unixcw): Likewise.
* gnu/packages/rust.scm (rust-1.32): Likewise.
* gnu/packages/security-token.scm (opensc): Likewise.
(python-pyscard): Likewise.
* gnu/packages/selinux.scm (python-setools): Likewise.
* gnu/packages/spice.scm (libcacard): Likewise.
* gnu/packages/telephony.scm (libtgvoip): Likewise.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès 425ccde6ae
gnu: Use 'search-input-directory' when looking for C/C++ library headers. 
* gnu/packages/arcan.scm (arcan)[arguments]: Use
'search-input-directory' for "include/libdrm" and "include/apr-1".
* gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish.
* gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers.
* gnu/packages/cedille.scm (cedille): Likewise for IAL headers.
* gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx
headers.
* gnu/packages/cups.scm (hplip): Likewise for libusb headers.
* gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers.
* gnu/packages/game-development.scm (python2-renpy): Likewise for
fribidi headers.
* gnu/packages/games.scm (pokerth): Likewise for libircclient.
* gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile.
* gnu/packages/hurd.scm (hurd): Likewise for libtirpc.
* gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for
libcxx, catch2, and nlohmann-json-cpp.
* gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's
errno.h.
* gnu/packages/kde-pim.scm (kdepim-runtime): Use
'search-input-directory' for "include/KF5".
(kmessagelib): Likewise.
* gnu/packages/kde.scm (kdeconnect): Likewise.
* gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc.
* gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband".
* gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h"
and "aspell.h".
* gnu/packages/radio.scm (dream): Use 'search-input-file' and
'search-input-directory' for pulseaudio, sndfile, etc.
* gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and
libaudit.
* gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for
libcxx.
* gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5".
* gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest".
(libopenshot): Likewise for "include/UnitTest++".
* gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for
protobuf file.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès 1ec13efbd2
gnu: Use 'search-input-directory' for the Eigen header directory. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-directory' when searching for Eigen headers.
* gnu/packages/bioinformatics.scm (nanopolish): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
 2021-07-24 16:23:22 +02:00
Ludovic Courtès 6ea7297ea4
gnu: Use 'search-input-directory' when looking for tzdata. 
* gnu/packages/backup.scm (duplicity)[arguments]: Use
'search-input-directory' for "share/zoneinfo".
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Likewise.
(pigx-bsseq): Likewise.
* gnu/packages/calcurse.scm (calcurse): Likewise.
* gnu/packages/calendar.scm (date): Likewise.
* gnu/packages/compression.scm (lhasa): Likewise.
* gnu/packages/cran.scm (r-rstan): Likewise.
* gnu/packages/django.scm (python-django): Likewise.
* gnu/packages/dlang.scm (ldc-bootstrap): Likewise.
* gnu/packages/finance.scm (ledger): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/kde-frameworks.scm (kcalendarcore): Likewise.
(kdelibs4support): Likewise.
* gnu/packages/kodi.scm (kodi): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/perl.scm (perl-libtime-parsedate): Likewise.
* gnu/packages/python-xyz.scm (python-robotframework): Likewise.
(python-dparse): Likewise.
* gnu/packages/rrdtool.scm (rrdtool): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/vim.scm (vim): Likewise.
* gnu/packages/virtualization.scm (ganeti): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
* gnu/packages/xfce.scm (xfce4-panel): Likewise.
* gnu/packages/mate.scm (libmateweather): Use 'search-input-file' for
"share/zoneinfo/zone.tab".
 2021-07-24 16:23:22 +02:00
Efraim Flashner fd8aea010f
gnu: python-pysam: Make the check phase honor the tests? argument. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
 2021-07-22 10:58:22 +03:00
Efraim Flashner 877792a6a7
gnu: python-pysam: Update to 0.16.0.1. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
 2021-07-22 10:57:41 +03:00
Efraim Flashner cc4906d13b
gnu: Add htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
 2021-07-22 10:50:58 +03:00
Efraim Flashner 309b38bed6
gnu: python-biopython: Update to 1.73. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
 2021-07-22 09:14:12 +03:00
Lars-Dominik Braun 73830b5da3
gnu: Add r-battenberg. 
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun ed636babfa
gnu: Add r-ascat. 
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 690df95d1a
gnu: Add nanosv. 
* gnu/packages/bioinformatics.scm (nanosv): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 2b665b8a49
gnu: Add python-pyvcf. 
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 086c6800cf
gnu: checkm: Rename and update to 1.1.3. 
Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.

* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun 18a02fe7ca
gnu: Add tombo. 
* gnu/packages/bioinformatics.scm (tombo): New variable.
 2021-07-21 13:36:07 +02:00
Ludovic Courtès 0e47fcced4
Merge branch 'master' into core-updates 2021-07-18 19:50:01 +02:00
Julien Lepiller ef79d6c5d6
gnu: Add ocaml-sqlite3. 
* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
(ocaml4.07-sqlite3): Inherit from ocaml-sqlite3.
* gnu/packages/bioinformatics.scm (pplacer): Also use package-with-ocaml4.07
with ocaml-sqlite3.
 2021-07-05 16:54:11 +02:00
Ludovic Courtès ebb8e44a4a
gnu: bioperl-minimal: Avoid top-level cross-module references. 
This could lead to circular reference breakage.

* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
 2021-07-01 17:13:13 +02:00
Ludovic Courtès b17ee44212
gnu: Do not import (gnu packages commencement). 
Line introduced in 4efbf56e53.

* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
 2021-07-01 17:13:13 +02:00
Tobias Geerinckx-Rice 9dea3f101f
Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/cups.scm
	gnu/packages/python-web.scm
	gnu/packages/web.scm
	guix/build/maven/pom.scm
 2021-06-23 18:45:21 +02:00
Efraim Flashner 07d2c72d39
gnu: ensembl-vep: Use a source file-name. 
* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
 2021-06-22 13:49:05 +03:00
Ricardo Wurmus 44bccf414b
gnu: Add perl-cworld-dekker. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
 2021-06-22 08:40:56 +02:00
Ricardo Wurmus 8a62d8685a
gnu: Add python-iced. 
* gnu/packages/bioinformatics.scm (python-iced): New variable.
 2021-06-21 13:02:39 +02:00
Marius Bakke 6f9a80b331
Merge branch 'master' into core-updates 
Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a277 and
12964df69a respectively.

4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.

 Conflicts:
	gnu/local.mk
	gnu/packages/aidc.scm
	gnu/packages/boost.scm
	gnu/packages/curl.scm
	gnu/packages/nettle.scm
	gnu/packages/networking.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tls.scm
 2021-06-19 17:38:47 +02:00
Ricardo Wurmus 748d3a2b8a
gnu: Add python-cgatcore. 
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
 2021-06-14 23:13:56 +02:00
Maxim Cournoyer ea0a51071e
gnu: Rename qtbase to qtbase-5. 
This change was automated via the following command:

$ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g'
$ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g'
$ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g'
$ git checkout etc    # to clear some spurious changes

This is done so the qtbase package can be upgraded to version 6 in the
following commit.
 2021-06-14 00:24:42 -04:00
Ricardo Wurmus ac51eb1125
gnu: pigx-sars-cov2-ww: Update to 0.0.2. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
 2021-06-08 22:43:47 +02:00
Ricardo Wurmus c9e8e7b0bf
gnu: pigx-bsseq: Update to 0.1.5. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
 2021-06-08 16:35:17 +02:00
Mădălin Ionel Patrașcu dd3698c1ac
gnu: python-hicmatrix: Update to 15. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-06-08 16:35:17 +02:00
Efraim Flashner 61bce4d143
gnu: python-mappy: Move to (gnu packages bioinformatics). 
* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
 2021-06-08 09:50:55 +03:00
Ricardo Wurmus 4a01e00a13
gnu: pigx-rnaseq: Update to 0.0.17. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
 2021-06-08 00:53:06 +02:00
Ricardo Wurmus be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus bb38287570
gnu: salmon: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 9875dae429
gnu: macs: Update to 2.2.7.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 1ace395f9c
gnu: libgff: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 176513f5f3
gnu: jellyfish: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 1ac8f05103
gnu: multiqc: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
 2021-06-07 10:53:16 +02:00
Mădălin Ionel Patrașcu a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3. 
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Marius Bakke 8d59c262ad
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/algebra.scm
	gnu/packages/bioinformatics.scm
	gnu/packages/curl.scm
	gnu/packages/docbook.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/maths.scm
	gnu/packages/plotutils.scm
	gnu/packages/python-web.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/readline.scm
	gnu/packages/tls.scm
	gnu/packages/xml.scm
	gnu/packages/xorg.scm
 2021-06-06 21:16:32 +02:00
Efraim Flashner b65c02e2d3
gnu: freebayes: Update to 1.3.5. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-06-06 12:13:28 +03:00
Mădălin Ionel Patrașcu d1e7b50dbf
gnu: python-cooler: Update to 0.8.11. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
 2021-06-06 08:33:21 +02:00
Ricardo Wurmus f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
 2021-06-05 09:12:39 +02:00
Roel Janssen 7382aa00b8
gnu: python-scanpy: Update to 1.7.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
 2021-06-04 23:51:35 +02:00
Maxime Devos b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (nanopolish)[arguments]<#:phases>{wrap-programs}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:33 +02:00
Maxime Devos 2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (gess)[arguments]<#:phases>{install}
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:32 +02:00
Maxime Devos c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (prinseq)[arguments]<#:phases>{install}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:32 +02:00
Maxime Devos fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'. 
* gnu/packages/bioinformatics.scm
  (proteinortho)[arguments]<#:phases>{wrap-programs}:
  Set #:guile argument of ‘wrap-script’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-04 22:34:32 +02:00
Ricardo Wurmus d06ae05808
gnu: Add pigx-sars-cov2-ww. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
 2021-06-04 12:57:08 +02:00
Ricardo Wurmus 0928e55266
gnu: Add fit-sne. 
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
 2021-06-03 12:22:29 +02:00
Ricardo Wurmus 011d586c2c
gnu: Add biobambam2. 
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
 2021-06-02 13:54:15 +02:00
Ricardo Wurmus 18e0081045
gnu: Add libmaus2. 
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
 2021-06-02 13:54:15 +02:00
Roel Janssen 7ae2b1f2dc
gnu: Add bamutils. 
* gnu/packages/bioinformatics.scm (bamutils): New variable.
 2021-06-01 13:14:38 +02:00
Ricardo Wurmus f463f376e9
gnu: bits: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:10:20 +02:00
Ricardo Wurmus d1e1c02e28
gnu: piranha: Use git-version. 
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
 2021-05-31 16:10:00 +02:00
Ricardo Wurmus 8c033085cc
gnu: r-chipkernels: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:09:35 +02:00
Ricardo Wurmus 3acfbd4811
gnu: f-seq: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:09:07 +02:00
Ricardo Wurmus 09b50a6ec2
gnu: bismark: Use git-file-name. 
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
 2021-05-31 16:08:47 +02:00
Ricardo Wurmus f383f9e311
gnu: filevercmp: Use git-version. 
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
 2021-05-31 16:08:12 +02:00
Ricardo Wurmus a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
 2021-05-31 15:53:20 +02:00
Ricardo Wurmus b0ecd6cea9
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1. 
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 15:46:30 +02:00
zimoun c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
 2021-05-31 15:39:49 +02:00
zimoun 7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
 2021-05-31 15:39:49 +02:00
zimoun 36cb01066c
gnu: r-copyhelper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:39:47 +02:00
zimoun 31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun cc1dbea883
gnu: r-annotationfilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 7360dea624
gnu: r-rcas: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
 2021-05-31 15:38:59 +02:00
zimoun 043c309d15
gnu: r-rhtslib: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
 2021-05-31 15:38:59 +02:00
zimoun e0c81584ea
gnu: r-zlibbioc: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
 2021-05-31 15:38:58 +02:00
zimoun 0006a66415
gnu: r-seqlogo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
 2021-05-31 15:38:21 +02:00
zimoun c2a18aee16
gnu: r-motifrg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 621aa3b442
gnu: r-sva: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 900ef8fb1e
gnu: r-protgenerics: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 720d2694a5
gnu: r-mzr: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 88cf24febb
gnu: r-ensembldb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun fea33b9d1e
gnu: r-biovizbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 8d4311bb8e
gnu: r-vsn: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 96ae9822c4
gnu: r-affyio: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 8182e6a6fd
gnu: r-organismdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun d1ea2b7c8b
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 0b5b41c561
gnu: r-genomicfiles: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun ff65fa90d2
gnu: r-complexheatmap: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 84019edf38
gnu: r-gage: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun d0a5503752
gnu: r-keggrest: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 22cda2e432
gnu: r-affy: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 32ae36e96f
gnu: r-fastseg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 9644745692
gnu: r-annotationhub: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun dfe6224f5f
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun f6f43a2d40
gnu: r-edaseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun ef954bb488
gnu: r-deseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun bb118f20fe
gnu: r-aroma-light: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 7756e08b44
gnu: r-mzid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun ad46c8aa7f
gnu: r-pcamethods: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
 2021-05-31 15:37:57 +02:00
zimoun d7fa9c1ffd
gnu: r-genomationdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:37:55 +02:00
zimoun f8fe5497c7
gnu: r-genomation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
 2021-05-31 15:36:32 +02:00
zimoun f3b50aa4fd
gnu: r-go-db: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
 2021-05-31 15:35:53 +02:00
zimoun 14fb30e5f6
gnu: r-seqpattern: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
 2021-05-31 15:35:30 +02:00
zimoun b832fddbfc
gnu: r-impute: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
 2021-05-31 15:34:45 +02:00
zimoun 4f030cc0db
gnu: r-msnbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 8c7c78bfce
gnu: r-msnid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 537d48d869
gnu: r-bsgenome: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 90bbab5cff
gnu: r-topgo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun f78ff75b41
gnu: r-genomicfeatures: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun a88230a1bc
gnu: r-rtracklayer: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun ca1a015777
gnu: r-genomicalignments: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
 2021-05-31 15:34:39 +02:00
Ricardo Wurmus e3cde9aaf8
gnu: Add mosaicatcher. 
* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-29 07:26:15 +02:00
Christopher Baines 6417b97c7e
Revert "gnu: Add mosaicatcher." 
mosaicatcher-unbundle-htslib.patch is missing.

This reverts commit b1ae0f30d8.
 2021-05-29 01:21:14 +01:00
Ricardo Wurmus b1ae0f30d8
gnu: Add mosaicatcher. 
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-28 23:00:47 +02:00
Roel Janssen 87c9f63fce
gnu: Add python-pyega3. 
* gnu/packages/bioinformatics.scm (python-pyega3): New variable.
 2021-05-27 23:01:35 +02:00
Roel Janssen a30e616ccc
gnu: Add python-htsget. 
* gnu/packages/bioinformatics.scm (python-htsget): New variable.
 2021-05-27 22:50:46 +02:00
Efraim Flashner c5f7203e3e
gnu: minimap2: Install more files. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules.
Adjust custom 'install phase to also install library, headers and a
pkg-config file.
 2021-05-26 15:22:10 +03:00
Efraim Flashner 36a90d0637
gnu: minimap2: Update to 2.18. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.18.
[source]: Remove patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-05-26 15:22:10 +03:00
Roel Janssen af163badb4
gnu: Add r-phantompeakqualtools. 
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable.
 2021-05-26 09:34:37 +02:00
Roel Janssen b1fee8a003
gnu: Add r-spp. 
* gnu/packages/bioinformatics.scm (r-spp): New variable.
 2021-05-26 09:29:01 +02:00
Marius Bakke 4ea6852c5f
Merge branch 'master' into core-updates 2021-05-22 17:21:57 +02:00
Ricardo Wurmus 7ff515aa51
gnu: r-rhdf5filters: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Update to 1.2.1.
 2021-05-20 14:43:34 +02:00
Ricardo Wurmus 48b8a5e701
gnu: pigx-chipseq: Update to 0.0.52. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.52.
 2021-05-17 18:45:55 +02:00
Ludovic Courtès 25487c3fe6
Merge branch 'master' into core-updates 2021-05-15 22:55:24 +02:00
Ricardo Wurmus 848126d008
gnu: prinseq: Fix references to perl executable. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Embed concrete
references to the "perl" executable.
 2021-05-14 17:11:52 +02:00
Marius Bakke f034264204
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/bioinformatics.scm
	gnu/packages/django.scm
	gnu/packages/gtk.scm
	gnu/packages/llvm.scm
	gnu/packages/python-web.scm
	gnu/packages/python.scm
	gnu/packages/tex.scm
	guix/build-system/asdf.scm
	guix/build/emacs-build-system.scm
	guix/profiles.scm
 2021-05-09 21:29:46 +02:00
Ricardo Wurmus 9b99b6d947
gnu: Add ensembl-vep. 
* gnu/packages/bioinformatics.scm (ensembl-vep): New variable.
 2021-05-07 08:52:49 +02:00
Ricardo Wurmus ce7b202f9b
gnu: Add perl-bio-db-hts. 
* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable.
 2021-05-06 18:56:24 +02:00
Ricardo Wurmus da7f89c737
gnu: python-pybedtools: Update to 0.8.2. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2.
[arguments]: Remove outdated substitutions; simplify check phase.
 2021-05-05 16:18:13 +02:00
Ricardo Wurmus 7694acebd1
gnu: r-summarizedexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here...
* gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here.
 2021-05-04 10:11:34 +02:00
Ricardo Wurmus d4051161e7
gnu: r-ensembldb: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 7072dc8c53
gnu: r-gage: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 3b002a49d4
gnu: r-annotationhub: Update to 2.22.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1.
 2021-05-04 09:47:36 +02:00
Roel Janssen f09e4dd8ea
gnu: Add pbgzip. 
* gnu/packages/bioinformatics.scm (pbgzip): New variable.
 2021-04-30 18:44:46 +02:00
Roel Janssen 7540f6915c
gnu: Update bedtools to 2.30.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
  [inputs]: Use latest samtools.
 2021-04-29 12:14:06 +02:00
Roel Janssen 558d11c3a8
gnu: Update samtools to 1.12. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
 2021-04-29 12:14:02 +02:00
Roel Janssen b904bb89a0
gnu: Update bcftools to 1.12. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
 2021-04-29 12:13:56 +02:00
Roel Janssen 241994230b
gnu: htslib: Update to 1.12. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
 2021-04-29 12:13:46 +02:00
Ricardo Wurmus e7707d5262
gnu: pigx-bsseq: Update to 0.1.3. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3.
[inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
 2021-04-28 21:58:05 +02:00
Ricardo Wurmus 01e33a031e
gnu: Add lofreq. 
* gnu/packages/bioinformatics.scm (lofreq): New variable.
 2021-04-28 17:41:47 +02:00
Ricardo Wurmus f01b3cd063
gnu: kraken2: Replace references to rsync. 
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
 2021-04-28 14:50:50 +02:00
Ricardo Wurmus 5ea5ea6066
gnu: Add python-pyliftover. 
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
 2021-04-28 10:52:12 +02:00
Vinicius Monego 76fb1a5cf2
gnu: Add python-louvain 0.15. 
* gnu/packages/graph.scm (python-louvain): Rename variable to
python-louvain-0.6.
(python-louvain): New variable.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Use
python-louvain-0.6.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2021-04-25 14:49:57 -04:00
Ricardo Wurmus f1f17c7bba
gnu: Add shorah. 
* gnu/packages/bioinformatics.scm (shorah): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus c9371b698d
gnu: Add r-shinycell. 
* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus 92032d8081
gnu: Add kraken2. 
* gnu/packages/bioinformatics.scm (kraken2): New variable.
 2021-04-22 08:31:17 +02:00
Roel Janssen c3926120ba
gnu: Update blast+ to 2.11.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.11.0.
 2021-04-16 20:56:43 +02:00
Efraim Flashner fcc39864db
Merge remote-tracking branch 'origin/master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/boost.scm
	gnu/packages/chez.scm
	gnu/packages/compression.scm
	gnu/packages/crates-io.scm
	gnu/packages/docbook.scm
	gnu/packages/engineering.scm
	gnu/packages/gcc.scm
	gnu/packages/gl.scm
	gnu/packages/gtk.scm
	gnu/packages/nettle.scm
	gnu/packages/python-check.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/rust.scm
	gnu/packages/sqlite.scm
	guix/build-system/node.scm
 2021-04-16 14:39:48 +03:00
Arun Isaac 563e4bd884
gnu: cwltool: Update to 3.0.20210319143721. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.0.20210319143721.
[arguments]: In the loosen-version-restrictions phase, relax pytest version
restriction. In the modify-tests phase, delete file tests/test_content_type.py
since it contains tests that require network access.
 2021-04-14 22:39:54 +05:30
Arun Isaac 12e210d907
gnu: python-schema-salad: Update to 7.1.20210316164414. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
7.1.20210316164414.
[arguments]: Add skip-failing-tests phase.
 2021-04-14 22:39:54 +05:30
Tobias Geerinckx-Rice e5852655b8
gnu: sortmerna: Mark up description. 
* gnu/packages/bioinformatics.scm (sortmerna)[description]: Use @acronym{}.
 2021-04-10 14:11:26 +02:00
Ricardo Wurmus 5f0c3535aa
gnu: r-genomicfeatures: Update to 1.42.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3.
 2021-04-08 13:28:24 +02:00
zimoun 23686ba3eb
Revert "Revert some commits that caused `guix pull` to fail." 
This reverts commit 8ec0ca8faf.
 2021-03-31 21:23:45 +02:00
Efraim Flashner 04ba7a196a
gnu: plink-ng: Build prettify binary. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to also build prettify.
 2021-03-31 14:33:42 +03:00
Efraim Flashner 5f3f2a7cc8
gnu: plink-ng: Remove custom install phase. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags and remove custom 'install phase.
 2021-03-31 14:33:34 +03:00
Efraim Flashner 977ea2c0a3
gnu: plink-ng: Sort inputs alphabetically. 
* gnu/packages/bioinformatics.scm (plink-ng)[inputs]: Sort
alphabetically.
 2021-03-31 14:32:43 +03:00
Efraim Flashner 58e9e0e142
gnu: plink-ng: Update to 2.00a2.3. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a2.3.
[arguments]: Adjust make-flags.
 2021-03-31 14:32:43 +03:00
Efraim Flashner 2aab587f84
Merge remote-tracking branch 'origin/master' into core-updates 2021-03-24 20:50:44 +02:00
Hong Li ee4fc3b662
gnu: Add r-signac. 
* gnu/packages/bioinformatics.scm (r-signac): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-03-22 14:27:17 +01:00
Mark H Weaver 1a265842e6
gnu: Use PACKAGE/INHERIT in more places. 
* gnu/packages/algebra.scm (fftwf, fftw-openmpi),
gnu/packages/audio.scm (ztoolkit-rsvg),
gnu/packages/bioinformatics.scm (python2-dendropy),
gnu/packages/boost.scm (boost-with-python2),
gnu/packages/check.scm (python2-mock, python2-pytest-mock),
gnu/packages/cups.scm (hplip-minimal),
gnu/packages/freedesktop.scm (libinput-minimal),
gnu/packages/gettext.scm (gnu-gettext),
gnu/packages/glib.scm (python2-pygobject),
gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi),
gnu/packages/groff.scm (groff-minimal),
gnu/packages/jami.scm (ffmpeg-jami),
gnu/packages/libcanberra.scm (libcanberra/gtk+-2),
gnu/packages/lirc.scm (python2-lirc),
gnu/packages/llvm.scm (clang-runtime-3.5),
gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple),
gnu/packages/node.scm (libnode),
gnu/packages/onc-rpc.scm (libtirpc/hurd),
gnu/packages/python-compression.scm (bitshuffle-for-snappy),
gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography)
(python2-cryptography, python2-m2crypto),
gnu/packages/python-web.scm (python2-html2text, python2-tornado)
(python2-terminado, python2-ndg-httpsclient, python2-websocket-client)
(python2-rauth, python2-url, python2-s3transfer),
gnu/packages/python-xyz.scm (python2-psutil, python2-serpent)
(python2-humanfriendly, python2-empy, python2-parse-type, python2-polib)
(python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc)
(python2-ipyparallel, python2-traitlets, python2-dbus)
(python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse)
(python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal)
(python2-contextlib2, python2-promise, python2-anyjson, python2-amqp)
(python2-kombu, python2-billiard, python2-celery, python2-whoosh)
(python2-jellyfish, python-rope, ptpython-2, python2-binaryornot)
(python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort)
(python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash)
(python2-cloudpickle, python2-reparser),
gnu/packages/python.scm (python2-called-python),
gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt)
(python-qscintilla, python-pyqt+qscintilla),
gnu/packages/scanner.scm (sane-backends),
gnu/packages/sdl.scm (guile3.0-sdl2),
gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc)
(python-sepolgen, policycoreutils),
gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack),
gnu/packages/simulation.scm (fenics),
gnu/packages/statistics.scm (python2-statsmodels),
gnu/packages/texinfo.scm (info-reader),
gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1),
gnu/packages/xml.scm (xmlsec-nss),
gnu/packages/xorg.scm (uim-gtk, uim-qt),
guix/build-system/python.scm (package-with-explicit-python)
(strip-python2-variant): Use PACKAGE/INHERIT.
 2021-03-17 03:58:10 -04:00
Ricardo Wurmus fcf8c6c565
gnu: hisat2: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.
 2021-03-16 11:12:01 +01:00
Leo Famulari 8ec0ca8faf
Revert some commits that caused `guix pull` to fail. 
This reverts commits 821e643921 through
8f9fd9b70c.

Specifically, these commits caused the build failure of
guix-package-cache.drv like this:

------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
 2021-03-15 19:52:34 -04:00
zimoun d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun adf45daae9
gnu: r-rsamtools: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 821e643921
gnu: r-limma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
 2021-03-15 23:30:26 +01:00
Ricardo Wurmus 14204d696c
gnu: r-genomicfeatures: Update to 1.42.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus f10f2745eb
gnu: r-delayedarray: Update to 0.16.2. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
 2021-03-15 15:03:08 +01:00
zimoun bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
 2021-03-15 14:06:24 +01:00
zimoun 082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
 2021-03-15 14:06:16 +01:00
zimoun 35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
 2021-03-15 14:05:56 +01:00
zimoun 8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
 2021-03-15 14:05:47 +01:00
zimoun 9949f459bf
gnu: r-iranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
 2021-03-15 14:05:37 +01:00
zimoun d64e3a487b
gnu: r-s4vectors: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
 2021-03-15 14:05:27 +01:00
zimoun 852fa82d4c
gnu: r-bioccheck: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
 2021-03-15 14:05:22 +01:00
zimoun d5576b6eb7
gnu: r-grohmm: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
 2021-03-15 14:04:26 +01:00
zimoun 5ac55aea8b
gnu: r-biocstyle: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
 2021-03-15 14:03:21 +01:00
zimoun 134404b437
gnu: r-biocviews: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
 2021-03-15 14:03:18 +01:00
Ricardo Wurmus 6e0ed09e68
gnu: Add instrain. 
* gnu/packages/bioinformatics.scm (instrain): New variable.
 2021-03-15 11:43:20 +01:00
Ricardo Wurmus ad34eb222c
gnu: Add python-drep. 
* gnu/packages/bioinformatics.scm (python-drep): New variable.
 2021-03-15 11:43:20 +01:00
zimoun df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
 2021-03-12 14:45:55 +01:00
zimoun 8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun 373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
 2021-03-12 14:45:53 +01:00
Efraim Flashner 5ae7414860
gnu: Add bandage. 
* gnu/packages/bioinformatics.scm (bandage): New variable.
 2021-03-11 16:54:38 +02:00
Ricardo Wurmus 133a918923
gnu: trim-galore: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6.
 2021-03-09 11:54:59 +01:00
Ricardo Wurmus 49d85b3f11
gnu: bbmap: Update to 38.90. 
* gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
 2021-03-09 11:54:59 +01:00
Nicolas Goaziou ea8e89292c
gnu: seqan-1: Use HTTPS source URI. 
* gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
 2021-03-06 16:05:44 +01:00
Nicolas Goaziou e062572812
gnu: seqan: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
 2021-03-06 16:01:24 +01:00
Christopher Baines a8448da0f4
Merge branch 'master' into core-updates 2021-03-06 00:18:30 +00:00
Ricardo Wurmus f5c3e8e2ec
gnu: Add r-cellchat. 
* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
 2021-03-05 15:04:15 +01:00
Tim Howes dcee10506c
gnu: infernal: Update to 1.1.4. 
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-03 10:11:51 +02:00
Tim Howes 9f4ffc249f
gnu: hmmer: Update to 3.3.2. 
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-03 10:11:51 +02:00
Ricardo Wurmus f21c711a0f
gnu: kallisto: Update to 0.46.2. 
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2.
[source]: Remove bundled htslib sources.
 2021-03-02 17:06:58 +01:00
Ricardo Wurmus cc39e9dbdc
gnu: kallisto: Use older htslib. 
* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead
of the latest.
 2021-03-02 17:06:58 +01:00
Nicolas Goaziou 3759df574d
gnu: f-seq: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
 2021-02-28 11:03:56 +01:00
Ricardo Wurmus 5d5bbd6fcc
gnu: Add star-for-pigx. 
This is a follow-up to commit f1f6e49190.

* gnu/packages/bioinformatics.scm (star-for-pigx): New variable.
(pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
 2021-02-23 19:40:59 +01:00
Ricardo Wurmus f1f6e49190
gnu: star: Update to 2.7.8a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
 2021-02-22 21:16:19 +01:00
Ricardo Wurmus f310b06685
gnu: nanopolish: Fix script wrapping. 
* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
 2021-02-19 23:35:04 +01:00
Ricardo Wurmus 15c0cc4aa2
gnu: Add prinseq. 
* gnu/packages/bioinformatics.scm (prinseq): New variable.
 2021-02-19 23:14:59 +01:00
Ricardo Wurmus 80d3150c94
gnu: Add ngshmmalign. 
* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
 2021-02-19 17:24:52 +01:00