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Author SHA1 Message Date
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
Ricardo Wurmus
8360705948
gnu: Add r-archr. 
* gnu/packages/bioinformatics.scm (r-archr): New variable.
 2021-02-18 16:11:38 +01:00
Ricardo Wurmus
9904a15a4c
gnu: Add indelfixer. 
* gnu/packages/bioinformatics.scm (indelfixer): New variable.
 2021-02-15 13:51:58 +01:00
Mădălin Ionel Patrașcu
160e4a95e7
gnu: bowtie1: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0.
[arguments]: Set CC in make flags.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-02-11 22:29:37 +01:00
Ricardo Wurmus
0e3e26ca60
gnu: r-gage: Update to 2.40.1. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
5103da059a
gnu: r-msnbase: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
2596200514
gnu: r-methylkit: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
3f7e96acc7
gnu: r-delayedarray: Update to 0.16.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
9b66b8017d
gnu: r-biomart: Update to 2.46.3. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
8e25b1acf9
gnu: r-edger: Update to 3.32.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
809f725977
gnu: r-iranges: Update to 2.24.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
88fd569ddf
gnu: r-s4vectors: Update to 0.28.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
babb2dce34
gnu: r-systempiper: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
d3ac91dd9d
gnu: r-gseabase: Update to 1.52.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
074d142ab6
gnu: r-genefilter: Update to 1.72.1. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1.
 2021-02-11 21:33:37 +01:00
Danny Milosavljevic
abd318ff4b
Merge branch 'master' into core-updates 2021-02-11 19:12:36 +01:00
Ricardo Wurmus
8d61539883
gnu: rsem: Link with shared libhts library. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so
instead of libhts.a.
 2021-02-05 23:30:43 +01:00
Christopher Baines
e740cc6140
Merge branch 'master' into core-updates 2021-02-03 09:57:35 +00:00
Efraim Flashner
877ab0266c
gnu: vcflib: Fix generated pkg-config file. 
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
 2021-02-01 19:02:14 +02:00
Maxim Cournoyer
d42245d401
gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH. 
This change was automated using:

$ git ls-files | grep .scm | \
  xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i

$ git ls-files | grep .scm | \
  xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i

* gnu/packages/admin.scm (nmap):
(dstat): Wrap using GUIX_PYTHONPATH.
* gnu/packages/audio.scm (jack-2):
(carla): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (couger): Likewise.
(gess, find-circ, filtlong, nanopolish): Likewise.
* gnu/packages/cdrom.scm (cdemu-client): Likewise.
* gnu/packages/chemistry.scm (avogadro): Likewise.
* gnu/packages/connman.scm (econnman): Likewise.
* gnu/packages/cups.scm (hplip): Likewise.
* gnu/packages/debug.scm (scanmem): Likewise.
* gnu/packages/display-managers.scm (lightdm): Likewise.
* gnu/packages/ebook.scm (cozy): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/engineering.scm (kicad, volk, freecad): Likewise.
* gnu/packages/game-development.scm (renpy): Likewise.
* gnu/packages/games.scm (roguebox-adventures)
(seahorse-adventures, kajongg): Likewise.
* gnu/packages/gimp.scm (gimp, glimpse): Likewise.
* gnu/packages/glib.scm (itstool): Likewise.
* gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise.
(eolie, d-feet, gedit, caribou, gnome-shell, authenticator)
(gnome-todo, orca, passwordsafe, terminator, setzer)
(libratbag, komikku): Likewise.
* gnu/packages/gps.scm (gpsd): Likewise.
* gnu/packages/gtk.scm (gtk-doc): Likewise.
* gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy)
(ibus-libhangul): Likewise.
* gnu/packages/inkscape.scm (inkscape-1.0): Likewise.
* gnu/packages/linux.scm (bcc): Likewise.
* gnu/packages/mail.scm (notifymuch): Likewise.
* gnu/packages/maths.scm (units): Likewise.
* gnu/packages/music.scm (solfege): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/patchutils.scm (patchwork): Likewise.
* gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/presentation.scm (presentty): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/storage.scm (ceph): Likewise.
* gnu/packages/syndication.scm (liferea): Likewise.
* gnu/packages/task-management.scm (blanket): Likewise.
* gnu/packages/text-editors.scm (manuskript): Likewise.
* gnu/packages/version-control.scm (gitless, cgit, git-when-merged)
(git-imerge): Likewise.
* gnu/packages/video.scm (pitivi): Likewise.
* gnu/packages/virtualization.scm (criu): Likewise.
* gnu/packages/xfce.scm (catfish): Likewise.
 2021-02-01 11:54:01 -05:00
Maxim Cournoyer
44db90b39f
gnu: python-loompy: Do not set PYTHONPATH. 
* gnu/packages/bioinformatics.scm (python-loompy)
[phases]{check}: Do not set PYTHONPATH.
 2021-02-01 11:53:47 -05:00
Maxim Cournoyer
21ce20bd2f
gnu: python-scanpy: Do not set PYTHONPATH. 
* gnu/packages/bioinformatics.scm (python-scanpy)[phases]
{check}: Do not set PYTHONPATH.
 2021-02-01 11:53:47 -05:00
Maxim Cournoyer
3c0b373310
gnu: python-screed: Adjust following Python build system changes. 
* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no
longer necessary.
 2021-02-01 11:53:47 -05:00
Maxim Cournoyer
5e47bebf3b
gnu: bamm: Update following changes to the Python build system. 
* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t.
[phases]{check}: Override rather than delete phase.  Remove trailing #t.
{post-install-check}: Delete phase.
{wrap-executable}: Also wrap with the new GUIX_PYTHONPATH.
 2021-02-01 11:53:46 -05:00
Maxim Cournoyer
98769a7709
gnu: python-pysam: Adjust following Python build system changes. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the
'#:modules' argument.
[phases]: Remove trailing #t.
{check}: Do not manually set PYTHONPATH.
 2021-02-01 11:53:46 -05:00
Maxim Cournoyer
25798ca0e0
gnu: python-pybedtools: Streamline following Python build system changes. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.
 2021-02-01 11:53:46 -05:00
Maxim Cournoyer
82f5f6b14c
gnu: Replace all uses of texlive-union by texlive-updmap.cfg. 
* doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg.
* gnu/packages/algebra.scm (pari-gp): Likewise.
* gnu/packages/bioinformatics.scm (discrover, velvet): Likewise.
* gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise.
* gnu/packages/engineering.scm (fastcap): Likewise.
* gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise.
* gnu/packages/lisp.scm (sbcl): Likewise.
* gnu/packages/maths.scm (octave, hypre): Likewise.
* gnu/packages/music.scm (lilypond): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)
(python-matplotlib-documentation, python-ipython-documentation)
(python-pypandoc): Likewise.
* gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise.
* gnu/packages/scheme.scm (mit-scheme): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/tex.scm (simple-texlive-package)
(texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise.
 2021-01-29 13:35:47 -05:00
Maxim Cournoyer
23a5dcce1d
gnu: grocsvs: Remove package. 
This package depends on Python 2 and doesn't build anymore.  Upstream doesn't
seem active, but if they ever port it to Python 3, they should let people know
here: https://github.com/grocsvs/grocsvs/issues/6.

* gnu/packages/bioinformatics.scm (grocsvs): Delete.
 2021-01-29 10:58:25 -05:00
Ricardo Wurmus
c4a2cbeb06
gnu: Add r-demultiplex. 
* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
 2021-01-28 22:24:51 +01:00
Ricardo Wurmus
04b1a1f6bd
gnu: Add repeat-masker. 
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
 2021-01-28 15:07:55 +01:00
Ricardo Wurmus
6d3cafa086
gnu: Add trf. 
* gnu/packages/bioinformatics.scm (trf): New variable.
 2021-01-28 15:07:55 +01:00
Efraim Flashner
b3e39a475f
gnu: freebayes: Update source, home-page URIs. 
* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
 2021-01-19 11:48:38 +02:00