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
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
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
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
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
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
5ae7414860
gnu: Add bandage.
...
* gnu/packages/bioinformatics.scm (bandage): New variable.
2021-03-11 16:54:38 +02:00
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
49d85b3f11
gnu: bbmap: Update to 38.90.
...
* gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
2021-03-09 11:54:59 +01:00
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
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
a8448da0f4
Merge branch 'master' into core-updates
2021-03-06 00:18:30 +00:00
f5c3e8e2ec
gnu: Add r-cellchat.
...
* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
2021-03-05 15:04:15 +01:00
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
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
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
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
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
5d5bbd6fcc
gnu: Add star-for-pigx.
...
This is a follow-up to commit f1f6e49190
2021-02-23 19:40:59 +01:00
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
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
15c0cc4aa2
gnu: Add prinseq.
...
* gnu/packages/bioinformatics.scm (prinseq): New variable.
2021-02-19 23:14:59 +01:00
80d3150c94
gnu: Add ngshmmalign.
...
* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
2021-02-19 17:24:52 +01:00
8360705948
gnu: Add r-archr.
...
* gnu/packages/bioinformatics.scm (r-archr): New variable.
2021-02-18 16:11:38 +01:00
9904a15a4c
gnu: Add indelfixer.
...
* gnu/packages/bioinformatics.scm (indelfixer): New variable.
2021-02-15 13:51:58 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
abd318ff4b
Merge branch 'master' into core-updates
2021-02-11 19:12:36 +01:00
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
e740cc6140
Merge branch 'master' into core-updates
2021-02-03 09:57:35 +00:00
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
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
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
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
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
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
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
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
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
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
c4a2cbeb06
gnu: Add r-demultiplex.
...
* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
2021-01-28 22:24:51 +01:00
04b1a1f6bd
gnu: Add repeat-masker.
...
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
2021-01-28 15:07:55 +01:00
6d3cafa086
gnu: Add trf.
...
* gnu/packages/bioinformatics.scm (trf): New variable.
2021-01-28 15:07:55 +01:00
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
99043adf46
gnu: freebayes: Don't include vcflib sources.
...
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove
vcflib-source, intervaltree-source. Move vcflib ...
[inputs]: ... to here.
[arguments]: Adjust 'patch-source and 'unpack-submodule-sources for
changes in vendored code.
* gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
2021-01-19 11:41:07 +02:00
1bbfe1789d
gnu: vcflib: Add pkg-config file.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
2021-01-19 11:36:01 +02:00
d6a8148c8d
gnu: vcflib: Build a shared library.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
2021-01-19 10:43:06 +02:00
797585746b
gnu: freebayes: Extend test timeout on slower architectures.
...
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom
'check phase on aarch64-linux and armhf-linux to extend the test timeout.
2021-01-19 10:33:19 +02:00
c0afd8044f
gnu: Add r-snapatac.
...
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
2021-01-18 23:26:53 +01:00
2d9c6542c8
gnu: mafft: Update to 7.475.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18 11:57:28 +02:00
6cb86e23a9
gnu: ruby-bio-vcf: Rename to bio-vcf.
...
This package is widely known in select circles specifically as 'bio-vcf'.
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
2021-01-18 11:19:37 +02:00
9b6cddd32d
gnu: Add ruby-bio-vcf.
...
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
2021-01-18 10:41:46 +02:00
fc9fd5496f
gnu: freebayes: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3.
[source]: Add patch. Add snippet to remove vendored library.
[build-system]: Switch to meson-build-system.
[inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp.
[native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman
source, multichoose source, fsom source, filevercmp source, fastahack
source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib.
[arguments]: Drop make-flags. Don't delete 'configure phase. Delete
custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install
phases. Adjust 'unpack-submodule-sources phase to changed native-inputs.
Add new 'patch-source phase.
2021-01-17 15:47:32 +02:00
3ddeefe854
gnu: multichoose: Install header files.
...
* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust
'install phase to also install header files.
2021-01-17 15:47:32 +02:00
976603b909
gnu: filevercmp: Install header files.
...
* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust
'install phase to install header files.
2021-01-17 15:47:32 +02:00
93309e25c7
gnu: vcflib: Update to 1.0.2.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2.
[source]: Download using git-fetch. Remove patch. Update snippet to use
packaged libraries.
[build-system]: Switch to cmake-build-system.
[inputs]: Add bzip2.
[native-inputs]: Add package-source of fsom.
[arguments]: Delete custom 'set-flags, 'install phases. Don't delete
'configure phase. Adjust 'unpack-submodule-sources phase.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-01-14 20:43:31 +02:00
db30d6eada
gnu: sambamba Update to 0.8.0.
...
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0.
[source, home-page]: Update to new upstream URI.
[arguments]: Shorten 'fix-ldc-version phase. Remove
'place-biod-and-undead phase. Update 'unbundle-prerequisites and
'insatll phases.
[native-inputs]: Remove rdmd, biod. Move ldc ...
[inputs]: ... to here. Add zlib.
(htslib-for-sambamba): Remove variable.
2021-01-14 20:43:31 +02:00
2051be4f4c
gnu: gemma: Enable tests.
...
* gnu/packages/bioinformatics.scm (gemma)[source]: Add snippet to remove
bundled sources.
[native-inputs]: Add catch-framework2-1, perl, shunit2, which.
[arguments]: Don't disable tests. Override 'check phase.
2021-01-14 20:43:31 +02:00
daf96e704d
gnu: gemma: Add Texinfo markup.
...
* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
2021-01-14 20:43:30 +02:00
a36abbe005
gnu: gemma: Update to 0.98.3.
...
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3.
[source, home-page]: Update to new upstream URI.
[inputs]: Remove eigen, gfortran, lapack.
[arguments]: Remove make-flags. Remove 'find-eigen phase. Rename
'bin-mkdir phase to 'prepare-build and substitute openblas include
directory.
2021-01-14 20:43:30 +02:00
01f0707207
Merge branch 'staging' into 'core-updates'.
...
Conflicts:
gnu/local.mk
gnu/packages/cmake.scm
gnu/packages/curl.scm
gnu/packages/gl.scm
gnu/packages/glib.scm
gnu/packages/guile.scm
gnu/packages/node.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/python-xyz.scm
gnu/packages/python.scm
gnu/packages/tls.scm
gnu/packages/vpn.scm
gnu/packages/xorg.scm
2021-01-13 23:45:53 -05:00
610cd6a170
gnu: r-ggbio: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
2020-12-29 17:40:28 +01:00
81f481d6cd
gnu: r-gqtlstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29 17:40:28 +01:00
61ec8928c7
gnu: r-snpstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
2020-12-29 17:40:28 +01:00
a2c66d18a5
gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
2020-12-29 17:40:28 +01:00
8c2b7c9a2a
gnu: r-erma: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
2020-12-29 17:40:28 +01:00
8f1237c350
gnu: r-ldblock: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
2020-12-29 17:40:28 +01:00
9534e7b706
gnu: r-gqtlstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29 17:40:28 +01:00
2a4322f7c3
gnu: r-gviz: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
2020-12-29 17:40:28 +01:00
69a5e066c1
gnu: r-gwascat: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
2020-12-29 17:40:28 +01:00
838db0de5e
gnu: r-sushi: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
2020-12-29 17:40:25 +01:00
07e08bc7d5
gnu: discrover: Use new texlive package names.
...
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
"texlive-fonts-cm" and "texlive-fonts-amsfonts" with their new names
"texlive-cm" and "texlive-amsfonts", respectively.
2020-12-23 10:10:58 +01:00
714d02b6b5
gnu: discrover: Remove obsolete build phase.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove obsolete
build phase setenv-HOME.
2020-12-23 10:10:58 +01:00
6203b8e5bd
gnu: kentutils: Build with OpenSSL 1.1.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0
to OPENSSL.
2020-12-20 16:30:42 +01:00
ca27b0e528
gnu: kentutils: Add a file name for the "samtabix" input.
...
* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix",
add a file name on the origin.
2020-12-20 16:30:42 +01:00
48f77ecbb1
gnu: r-keggrest: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09 23:30:12 +01:00
4745f0dfca
gnu: r-genomeinfodb: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09 23:30:12 +01:00
baeaa02e75
gnu: r-biocstyle: Update to 2.18.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09 23:30:12 +01:00
4617cc7fd5
gnu: r-rhtslib: Propagate zlib.
...
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
(r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
r-methylkit)[inputs]: Remove zlib.
* gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
2020-12-09 12:12:48 +01:00
cde035e67f
gnu: r-gqtlstats: Update to 1.21.3.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
2020-12-09 12:12:48 +01:00
6a4818716d
gnu: r-gqtlbase: Update to 1.21.1.
...
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1.
[arguments]: Add phase to patch broken NAMESPACE file.
2020-12-09 12:12:48 +01:00
970984237a
gnu: r-biocviews: Update to 1.58.1.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1.
Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09 12:12:47 +01:00
53affb349a
gnu: r-rhdf5: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0.
[propagated-inputs]: Add r-rhdf5filters.
[arguments]: Avoid to have a plain directory on the list of libraries to
link.
Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09 12:12:46 +01:00
86fcceeae1
gnu: Add r-rhdf5filters.
...
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
2020-12-09 12:12:46 +01:00
60ad3c7b3b
gnu: r-genomationdata: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
2020-12-09 12:12:46 +01:00
e707820442
gnu: r-sushi: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
2020-12-09 12:12:45 +01:00
83129edfb7
gnu: r-gwascat: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0.
[propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and
r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and
r-rtracklayer.
2020-12-09 12:12:45 +01:00
717e53fdc0
gnu: r-gviz: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
2020-12-09 12:12:45 +01:00
0a8d08e887
gnu: r-ldblock: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
2020-12-09 12:12:45 +01:00
494010ad3e
gnu: r-erma: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
2020-12-09 12:12:45 +01:00
6e338901bf
gnu: r-snpstats: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
2020-12-09 12:12:45 +01:00
74a11b21be
gnu: r-ggbio: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
2020-12-09 12:12:45 +01:00
3c6eecdeed
gnu: r-biovizbase: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
2020-12-09 12:12:45 +01:00
6e182c237a
gnu: r-organismdbi: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
2020-12-09 12:12:44 +01:00
06fe3b7a53
gnu: r-ensembldb: Update to 2.14.0.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
2020-12-09 12:12:44 +01:00
8962a13afe
gnu: r-dirichletmultinomial: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
2020-12-09 12:12:44 +01:00
4ef1e375b4
gnu: r-complexheatmap: Update to 2.6.2.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2;
[propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and
r-s4vectors.
2020-12-09 12:12:44 +01:00
0fde2f9ad2
gnu: r-genomicfiles: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0.
[propagated-inputs]: Add r-matrixgenerics.
2020-12-09 12:12:44 +01:00
78cadd0fef
gnu: r-gage: Update to 2.40.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
2020-12-09 12:12:44 +01:00
143437c623
gnu: r-keggrest: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
2020-12-09 12:12:44 +01:00
b6dd0722c8
gnu: r-fastseg: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
2020-12-09 12:12:44 +01:00
a9dc755e67
gnu: r-annotationhub: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
2020-12-09 12:12:43 +01:00
3becce3ff3
gnu: r-interactivedisplaybase: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0.
2020-12-09 12:12:43 +01:00
8e55b9f502
gnu: r-edaseq: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0.
2020-12-09 12:12:43 +01:00
8db8a683b9
gnu: r-aroma-light: Update to 3.20.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0.
2020-12-09 12:12:43 +01:00
971f3a377c
gnu: r-msnid: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.24.0.
[propagated-inputs]: Add r-annotationdbi, r-annotationhub, r-biocgenerics,
r-biocstyle, r-biostrings, r-ggplot2, r-msmstests, r-purrr, r-rlang, r-runit,
r-stringr, r-tibble, and r-xtable.
2020-12-09 12:12:43 +01:00
2ed937e0aa
gnu: r-pcamethods: Update to 1.82.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0.
2020-12-09 12:12:43 +01:00
b47560c1cf
gnu: r-mzid: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0.
[propagated-inputs]: Remove r-rcpp.
2020-12-09 12:12:43 +01:00
75bdab83cc
gnu: r-vsn: Update to 3.58.0.
...
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0.
2020-12-09 12:12:42 +01:00
6a6f38b89e
gnu: r-affy: Update to 1.68.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0.
2020-12-09 12:12:42 +01:00
d6750c6587
gnu: r-affyio: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0.
2020-12-09 12:12:42 +01:00
471ceb5e5e
gnu: r-mzr: Fix linking.
...
* gnu/packages/bioinformatics.scm (r-mzr)[arguments]: Fix linking with rhdf5
libraries.
2020-12-09 12:12:42 +01:00
badb4678bd
gnu: r-mzr: Update to 2.24.1.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.24.1.
2020-12-09 12:12:42 +01:00
4d9e168db8
gnu: r-protgenerics: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.22.0.
2020-12-09 12:12:42 +01:00
858eb988a0
gnu: r-sva: Update to 3.38.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.38.0.
2020-12-09 12:12:42 +01:00
99bd4f2d7c
gnu: r-methylkit: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.0.
2020-12-09 12:12:42 +01:00
2ed79a0a42
gnu: r-copywriter: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.22.0.
2020-12-09 12:12:41 +01:00
36fd725b6f
gnu: r-chipseq: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.40.0.
2020-12-09 12:12:41 +01:00
cad3eb4eb4
gnu: r-annotationfilter: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.14.0.
2020-12-09 12:12:41 +01:00
ec0050c0a9
gnu: r-tximport: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.18.0.
2020-12-09 12:12:41 +01:00
6d5a4dd0a7
gnu: r-mutationalpatterns: Update to 3.0.1.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 3.0.1.
[native-inputs]: Add r-knitr.
[propagated-inputs]: Add r-bsgenome, r-dplyr, r-ggalluvial,
r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove
r-reshape2 and r-summarizedexperiment.
2020-12-09 12:12:41 +01:00
a823a74525
gnu: r-rcas: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.16.0.
2020-12-09 12:12:41 +01:00
2c15a1c502
gnu: r-bamsignals: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.22.0.
2020-12-09 12:12:41 +01:00
728369634f
gnu: r-rhtslib: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.22.0.
2020-12-09 12:12:41 +01:00
b0d85e36f1
gnu: r-zlibbioc: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.36.0.
2020-12-09 12:12:40 +01:00
329879b70c
gnu: r-seqlogo: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.56.0.
2020-12-09 12:12:40 +01:00
2a70c96e3d
gnu: r-genomation: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.22.0.
2020-12-09 12:12:40 +01:00
44bf116f03
gnu: r-seqpattern: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.22.0.
2020-12-09 12:12:40 +01:00
a180744b37
gnu: r-impute: Update to 1.64.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.64.0.
2020-12-09 12:12:40 +01:00
e2e11f095f
gnu: r-bsgenome: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.58.0.
2020-12-09 12:12:40 +01:00
6a7de43a58
gnu: r-topgo: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.42.0.
2020-12-09 12:12:40 +01:00
26e2184fc1
gnu: r-genomicfeatures: Update to 1.42.1.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.1.
2020-12-09 12:12:40 +01:00
92377e7fea
gnu: r-rtracklayer: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.50.0.
2020-12-09 12:12:39 +01:00
077e813657
gnu: r-genomicalignments: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.26.0.
2020-12-09 12:12:39 +01:00
3ca5b05474
gnu: r-variantannotation: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.36.0.
[propagated-inputs]: Add r-matrixgenerics.
2020-12-09 12:12:39 +01:00
8607a5394b
gnu: r-summarizedexperiment: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.20.0.
[propagated-inputs]: Add r-matrixgenerics.
2020-12-09 12:12:39 +01:00
9168ab0911
gnu: r-rsamtools: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.6.0.
2020-12-09 12:12:39 +01:00
5d60273b77
gnu: r-biostrings: Update to 2.58.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.58.0.
2020-12-09 12:12:39 +01:00
444b101dc2
gnu: r-biocparallel: Update to 1.24.1.
...
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.24.1.
2020-12-09 12:12:39 +01:00
4fac3fe67d
gnu: r-biomart: Update to 2.46.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.0.
2020-12-09 12:12:39 +01:00
f517365cef
gnu: r-annotationdbi: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.52.0.
2020-12-09 12:12:39 +01:00
9103041d13
gnu: r-biobase: Update to 2.50.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.50.0.
2020-12-09 12:12:38 +01:00
7641dba3e6
gnu: r-genomicranges: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.42.0.
2020-12-09 12:12:38 +01:00
d972ab690e
gnu: r-limma: Update to 3.46.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.46.0.
2020-12-09 12:12:38 +01:00
5996929b36
gnu: r-edger: Update to 3.32.0.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.0.
2020-12-09 12:12:38 +01:00
cde7fcedf9
gnu: r-genomeinfodb: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.0.
2020-12-09 12:12:38 +01:00
2ae3b7db24
gnu: r-bioccheck: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.26.0.
2020-12-09 12:12:38 +01:00
1160c83caf
gnu: r-biocstyle: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.0.
2020-12-09 12:12:38 +01:00
182a080127
gnu: r-biocviews: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.0.
2020-12-09 12:12:38 +01:00
16a4822a07
gnu: r-grohmm: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.24.0.
2020-12-09 12:12:37 +01:00
5598f53497
gnu: r-systempiper: Update to 1.24.2.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.2.
[propagated-inputs]: Add r-iranges.
2020-12-09 12:12:37 +01:00
a05bb428e4
gnu: r-shortread: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.48.0.
2020-12-09 12:12:37 +01:00
74204b48eb
gnu: r-gostats: Update to 2.56.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.56.0.
2020-12-09 12:12:37 +01:00
afbc8e1433
gnu: r-category: Update to 2.56.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.56.0.
2020-12-09 12:12:37 +01:00
03312f052a
gnu: r-gseabase: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.0.
2020-12-09 12:12:37 +01:00
7a57b229b6
gnu: r-rbgl: Update to 1.66.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.66.0.
2020-12-09 12:12:37 +01:00
4451918e3a
gnu: r-annotationforge: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.32.0.
2020-12-09 12:12:37 +01:00
a323c1e9b4
gnu: r-dexseq: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.36.0.
2020-12-09 12:12:37 +01:00
936227f144
gnu: r-deseq2: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.30.0.
2020-12-09 12:12:37 +01:00
64cf667e98
gnu: r-genefilter: Update to 1.72.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.0.
2020-12-09 12:12:36 +01:00
fafa94b065
gnu: r-delayedarray: Update to 0.16.0.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.0.
[propagated-inputs]: Add r-matrixgenerics; remove r-matrixstats.
2020-12-09 12:12:36 +01:00
cf6033ee6e
gnu: r-iranges: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.0.
2020-12-09 12:12:35 +01:00
57820475db
gnu: r-s4vectors: Update to 0.28.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.0.
2020-12-09 12:12:35 +01:00
724b770678
gnu: r-xvector: Update to 0.30.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.30.0.
2020-12-09 12:12:35 +01:00
1e536c307c
gnu: Update r-msnbase to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.0.
2020-12-09 12:12:27 +01:00
3832704aff
gnu: minimap2: Fix build on aarch64-linux.
...
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust
configure-flags to be better per-architecture.
[source]: Add patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2020-12-07 12:48:07 +02:00
f48cd014f3
gnu: minimap2: Prepare for cross compilation.
...
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Use
cc-for-target.
2020-12-07 12:48:01 +02:00
555677fdf7
gnu: java-picard-1.113: Use ant/java8.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use
ant/java8.
[inputs]: Replace ant with ant/java8.
2020-12-01 13:30:34 +01:00
80fbad4fe6
gnu: pigx-chipseq: Update to 0.0.51.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.51.
[inputs]: Add r-corrplot, r-deseq2, r-dt, r-ggrepel, r-gprofiler2, r-pheatmap,
and r-rsubread.
2020-11-30 22:39:34 +01:00
d3c1b5f66d
gnu: pigx-scrnaseq: Update to 1.1.7.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.7.
2020-11-30 22:39:34 +01:00
bff94a5a53
Merge branch 'master' into staging
2020-11-26 01:08:35 +01:00
4efbf56e53
gnu: tadbit: Update to 1.0.1.
...
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1.
[arguments]: Remove #:tests? and #:python arguments.
[phases]{fix-problems-with-setup.py}: Remove no longer needed steps.
{check}: Override phase.
[native-inputs]: Add glib and pkg-config.
[inputs]: Add python-future and python-h5py.
2020-11-24 02:20:32 -05:00
e7e73f750f
gnu: imp: Migrate to Python 3.
...
* gnu/packages/bioinformatics.scm (imp)
[arguments]: Enable tests by removing the #:tests? argument.
Specify the arguments to pass to the ctest test running via the
#:configure-flags argument.
[inputs]: Add cgal and opencv. Remove python-2. Move swig to...
[native-inputs]: ...here. Add python-wrapper.
[propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas,
python2-scikit-learn and python2-networkx by python-numpy, python-scipy,
python-pandas, python-scikit-learn and python-networkx, respectively.
2020-11-24 02:20:31 -05:00
87a027243f
Merge branch 'master' into staging
2020-11-23 23:39:47 +01:00
964bc9e5fe
gnu: Add cwltool.
...
* gnu/packages/bioinformatics.scm (cwltool): New variable.
2020-11-23 15:43:38 +02:00
7face25953
gnu: Add python-schema-salad.
...
* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
2020-11-23 15:43:37 +02:00
4e5e05d409
Merge branch 'master' into staging
2020-11-15 23:45:34 +01:00
e1fa3ea9fe
gnu: methyldackel: Update to 0.5.1.
...
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1.
[arguments]: Link with libbigwig.
[inputs]: Add curl and libbigwig; replace htslib with htslib-1.9.
2020-11-15 23:31:35 +01:00
37ba374a53
gnu: Fix build for python-pysam.
...
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9,
samtools-1.9, and bcftools-1.9.
2020-11-13 16:16:43 +01:00
ecc309c142
gnu: Add bcftools-1.9.
...
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
2020-11-13 16:14:01 +01:00
c3232fcc77
gnu: bedtools: Use samtools-1.9.
...
The build for bedtools with samtools 1.11 triggers a testsuite
failure which is reported here:
https://github.com/arq5x/bedtools2/issues/814
* gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
2020-11-13 14:49:31 +01:00
da4a38edad
gnu: Add samtools-1.9.
...
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
2020-11-13 14:49:27 +01:00
3ede804f6d
gnu: Add htslib-1.9.
...
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
2020-11-13 14:49:20 +01:00
a9a0d34874
Merge branch 'master' into staging
2020-11-11 00:02:32 +01:00
4b3a535770
gnu: macs: Remove generated code.
...
* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove
cython generated code.
[native-inputs]: Add python-cython.
2020-11-09 11:34:08 +02:00
4dcd19d3ff
gnu: macs: Update check phase.
...
* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check
phase before using custom 'check phase.
2020-11-09 11:34:08 +02:00
fa82adb5e0
gnu: macs: Update source, home-page URIs.
...
* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update
URIs to new location.
2020-11-09 11:34:08 +02:00
32787d6524
Merge branch 'master' into staging
...
Conflicts:
gnu/local.mk
gnu/packages/gdb.scm
gnu/packages/lisp-xyz.scm
gnu/packages/web-browsers.scm
2020-11-07 21:33:32 +01:00
bcbd536e3f
gnu: Update samtools to 1.11.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
2020-10-29 16:55:07 +01:00
04a49b4143
gnu: Update bcftools to 1.11.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
2020-10-29 16:55:03 +01:00
zimoun
Efraim Flashner
Ricardo Wurmus
Nicolas Goaziou
Christopher Baines
Tim Howes
Mădălin Ionel Patrașcu
Danny Milosavljevic
Maxim Cournoyer
Marius Bakke
Roel Janssen