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2046 Commits

Author SHA1 Message Date
Ricardo Wurmus 8a5f9d3d56
gnu: r-edger: Update to 3.26.6. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
 2019-08-06 15:48:59 +02:00
Brian Leung d9340de903
gnu: khmer: Make gzip timestamps writable. 
* gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase
to make gzip timestamps writable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-08-05 10:22:20 +03:00
Marius Bakke e4e2bef12d
gnu: prank: Update to 170427. 
* gnu/packages/bioinformatics.scm (prank): Update to 170427.
 2019-07-31 14:41:35 +02:00
Marius Bakke 6a2e54236e
Merge branch 'master' into core-updates 2019-07-31 14:28:56 +02:00
Ludovic Courtès 91f55717ab
gnu: Explicitly refer to 'guile-json-1' when needed. 
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change
'guile-json' to 'guile-json-1'.
* gnu/packages/ci.scm (cuirass)[inputs]: Likewise.
* gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise.
* gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise.
* gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise.
* gnu/packages/mail.scm (mumi)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise.
* gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise.
 2019-07-25 00:18:45 +02:00
Marius Bakke ccad0e4d69
Merge branch 'master' into core-updates 2019-07-22 18:58:48 +02:00
Ricardo Wurmus 6fd4c6b267
gnu: htslib: Propagate zlib. 
Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>.

* gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
 2019-07-22 14:24:51 +02:00
Marius Bakke bc2076f053
gnu: bpp: Use the default GCC. 
* gnu/packages/bioinformatics.scm (bpp-core, bpp-phyl, bpp-popgen, bpp-seq,
bppsuite)[inputs]: Remove GCC-5.
 2019-07-18 23:29:07 +02:00
Ludovic Courtès 64de896a71
Merge branch 'master' into core-updates 2019-07-17 15:51:10 +02:00
Marius Bakke 3549e23b25
gnu: nanopolish: Fix build with GCC 7. 
* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Preserve the
existing CPATH variable, if any.
 2019-07-17 15:13:57 +02:00
Marius Bakke f8e0d93ca3
gnu: salmon: Fix build with GCC 7. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Do not read from
CPLUS_INCLUDE_PATH, and add headers to CPATH only.
 2019-07-15 18:21:47 +02:00
Ricardo Wurmus 886986b744
gnu: Add python-ont-fast5-api. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): New variable.
 2019-07-15 12:18:01 +02:00
Marius Bakke 97149c5767
gnu: Adjust uses of C{,PLUS}_INCLUDE_PATH for GCC 7. 
These variables are no longer set in the build environment by default.  GCC
still respects these search paths and treats them as "system headers" so we
can continue to use them, just not expect them to be available.

* gnu/packages/mpi.scm (openmpi)[arguments]: Do not attempt to read from
C_INCLUDE_PATH, nor CPLUS_INCLUDE_PATH.
* gnu/packages/games.scm (kiki)[arguments]: Likewise.
* gnu/packages/networking.scm (hcxtools)[arguments]: Likewise.
* gnu/packages/synergy.scm (synergy)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (gemma, sailfish)[arguments]: Likewise.
* gnu/packages/maths.scm (dune-alugrid)[arguments]: Likewise.
 2019-07-14 18:13:34 +02:00
Ricardo Wurmus c1b87329bf
gnu: pigx-rnaseq: Update to 0.0.10. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.10.
 2019-07-13 13:51:52 +02:00
Marius Bakke fb9a23a3f3
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/python-xyz.scm
	gnu/packages/xml.scm
	guix/gexp.scm
	po/guix/POTFILES.in
 2019-07-12 01:03:53 +02:00
Tobias Geerinckx-Rice 48182cff03
gnu: r-biocinstaller: Remove entirely. 
This follows up on commit 0971f8bd88,
which led to ‘r-biocmanager: unbound variable’ errors.  See
<https://lists.gnu.org/archive/html/guix-devel/2019-07/msg00120.html>.

* gnu/packages/bioinformatics.scm (r-biocinstaller): Remove variable.
 2019-07-09 13:26:26 +02:00
Tobias Geerinckx-Rice 0971f8bd88
gnu: Remove r-biocinstaller. 
It requires R < 3.6 and is no longer supported.

* gnu/packages/bioinformatics.scm (r-biocinstaller): Define as
deprecated in favour of r-biocmanager.
 2019-07-08 16:13:11 +02:00
Tobias Geerinckx-Rice 1042e3481d
gnu: r-xbioc: Update to 0.1.16-1.6ff0670. 
This is needed to deprecate r-biocinstaller, which is no longer
distributed.

* gnu/packages/bioinformatics.scm (r-xbioc): Update to 0.1.16-1.6ff0670.
[propagated-inputs]: Replace deprecated r-biocinstaller with
r-biocmanager.
 2019-07-08 16:11:55 +02:00
Ricardo Wurmus b35af24938
gnu: nanopolish: Update to 0.11.1-1.6331dc4. 
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
 2019-07-05 15:10:38 +02:00
Robert Vollmert 6657b0711e
gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml. 
These are ghc-8.4-bundled packages, removing to avoid build
conflicts.

* gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove.
* gnu/packages/haskell-web.scm (ghc-xhtml): Remove.
* gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text.
* gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and
ghc-text.
* gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec.
(git-annex)[inputs]: Remove ghc-stm and ghc-text.
(ghc-sdl2)[inputs]: Remove ghc-text.
(ghc-sdl2-image)[inputs]: Remove ghc-text.
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm.
(ghc-tasty)[inputs]: Remove ghc-stm.
(ghc-tasty-rerun)[inputs]: Same.
(ghc-quickcheck-instances)[inputs]: Remove ghc-text.
(ghc-hedgehog)[inputs]: Remove ghc-stm.
* gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove
ghc-text.
* gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text.
(ghc-cookie)[inputs]: Same.
(ghc-http-types)[inputs]: Same.
(ghc-http)[inputs]: Remove ghc-parsec.
(ghc-http-client)[inputs]: Remove ghc-text.
(ghc-http2)[inputs]: Remove ghc-stm.
(ghc-http-conduit)[native-inputs]: Remove ghc-text.
(ghc-wai)[inputs]: Same.
(ghc-wai-extra)[inputs]: Same.
(ghc-warp)[inputs]: Remove ghc-stm and ghc-text.
(ghc-xss-sanitize)[native-inputs]: Remove ghc-text.
(ghc-css-text)[inputs]: Same.
(ghc-mime-types)[inputs]: Same.
(ghc-blaze-html)[inputs]: Same.
(ghc-aeson)[inputs]: Same.
(ghc-aeson-pretty)[inputs]: Same.
(ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-multipart)[inputs]: Remove ghc-parsec.
(ghc-uri-encode)[inputs]: Remove ghc-text.
(ghc-path-pieces)[inputs]: Same.
(ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-yesod-persistent)[inputs]: Remove ghc-text.
(ghc-yesod-form)[inputs]: Same.
(ghc-yesod)[inputs]: Same.
(ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-hxt)[inputs]: Remove ghc-parsec.
* gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text.
(ghc-double-conversion)[inputs]: Same.
(ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text.
[native-inputs]: Remove ghc-parsec.
(ghc-cgi)[inputs]: Remove ghc-parsec.
(hlint)[inputs]: Remove ghc-text.
(ghc-openglraw)[inputs]: Remove ghc-text.
(ghc-opengl)[inputs]: Same.
(ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text.
(ghc-hackage-security)[inputs]: Remove ghc-parsec.
(cabal-install)[inputs]: Remove ghc-stm.
(ghc-parsec-numbers)[inputs]: Remove ghc-parsec.
(ghc-safesemaphore)[inputs]: Remove ghc-stm.
(ghc-text-binary)[inputs]: Remove ghc-text.
(ghc-hashable)[inputs]: Remove ghc-text.
(ghc-transformers-base)[inputs]: Remove ghc-stm.
(ghc-indents)[inputs]: Remove ghc-parsec.
(ghc-regex-tdfa-rc)[inputs]: Same.
(ghc-regex-tdfa-text)[inputs]: Same.
(ghc-regex)[inputs]: Remove ghc-text.
(ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-attoparsec)[inputs]: Remove ghc-text.
(ghc-attoparsec-bootstrap)[inputs]: Same.
(ghc-zip-archive)[inputs]: Same.
(ghc-polyparse)[inputs]: Same.
(ghc-reducers)[inputs]: Same.
(ghc-xml)[inputs]: Same.
(ghc-feed)[inputs]: Same.
(ghc-exceptions)[inputs]: Remove ghc-stm.
(ghc-case-insensitive)[inputs]: Remove ghc-text.
(ghc-megaparsec)[inputs]: Same.
(ghc-network-uri)[inputs]: Remove ghc-parsec.
(ghc-monad-control)[inputs]: Remove ghc-stm.
(ghc-blaze-builder)[inputs]: Remove ghc-text.
(ghc-blaze-markup)[inputs]: Same.
(ghc-async)[inputs]: Remove ghc-stm.
(ghc-invariant)[inputs]: Same.
(ghc-statevar)[inputs]: Same.
(ghc-lens)[inputs]: Remove ghc-text.
(ghc-cheapskate)[inputs]: Same.
(ghc-semigroups)[inputs]: Same.
(ghc-semigroups-bootstrap)[inputs]: Same.
(ghc-fast-logger)[inputs]: Same.
(ghc-scientific)[inputs]: Same.
(ghc-scientific-bootstrap)[inputs]: Same.
(ghc-texmath)[inputs]: Remove ghc-parsec.
(ghc-highlighting-kate)[inputs]: Same.
(ghc-cmark)[inputs]: Remove ghc-text.
(ghc-cmark-gfm)[inputs]: Same.
(ghc-th-lift-instances)[inputs]: Same.
(ghc-yaml)[inputs]: Same.
(ghc-hslua)[inputs]: Same.
(ghc-hslua-module-text)[inputs]: Same.
(ghc-skylighting-core)[inputs]: Same.
(ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-pandoc)[inputs]: Same.
(ghc-typed-process)[inputs]: Remove ghc-stm.
(ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text.
(ghc-xml-types)[inputs]: Remove ghc-text.
(ghc-xml-conduit)[inputs]: Same.
(ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-regex-tdfa)[inputs]: Remove ghc-parsec.
(ghc-wl-pprint-text)[inputs]: Remove ghc-text.
(ghc-graphviz)[inputs]: Same.
(ghc-system-filepath-bootstrap)[inputs]: Same.
(ghc-system-fileio-bootstrap)[inputs]: Same.
(ghc-shelly)[inputs]: Same.
(ghc-chell)[inputs]: Same.
(ghc-system-filepath)[inputs]: Same.
(ghc-system-fileio)[inputs]: Same.
(ghc-fsnotify)[inputs]: Same.
(ghc-json)[inputs]: Remove ghc-text and ghc-parsec.
(ghc-esqueleto)[inputs]: Remove ghc-text.
(shellcheck)[inputs]: Remove ghc-parsec.
(ghc-errors)[inputs]: Remove ghc-text.
(ghc-chunked-data)[inputs]: Same.
(ghc-uuid-types)[inputs]: Same.
(ghc-uuid)[inputs]: Same.
(ghc-rebase)[inputs]: Remove ghc-stm and ghc-text.
(ghc-foldl)[inputs]: Remove ghc-text.
(ghc-mono-traversable)[inputs]: Same.
(ghc-conduit-combinators)[inputs]: Same.
(ghc-aws)[inputs]: Same.
(ghc-stm-chans)[inputs]: Remove ghc-stm.
(ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm.
(ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text.
(ghc-resource-pool)[inputs]: Remove ghc-stm.
(ghc-attoparsec-iso8601)[inputs]: Remove ghc-text.
(ghc-http-api-data)[inputs]: Same.
(ghc-persistent)[inputs]: Same.
(ghc-aeson-compat)[inputs]: Same.
(ghc-persistent-template)[inputs]: Same.
(ghc-unliftio)[inputs]: Remove ghc-stm.
(ghc-persistent-sqlite)[native-inputs]: Remove ghc-text.
(ghc-bytes)[inputs]: Same.
(ghc-missingh)[inputs]: Remove ghc-parsec.
(ghc-rio)[inputs]: Remove ghc-text.
(ghc-cairo)[inputs]: Same.
(ghc-atomic-write)[inputs]: Remove ghc-text.
[native-inputs]: Same.
(ghc-stm-conduit)[inputs]: Remove ghc-stm.
(ghc-conduit-algorithms)[inputs]: Same.
(ghc-interpolate)[native-inputs]: Remove ghc-text.
(ghc-hpack)[inputs]: Same.
(ghc-inline-c)[inputs]: Remove ghc-parsec.
(ghc-configurator)[inputs]: Remove ghc-text.
(ghc-c2hs)[native-inputs]: Same.
(ghc-libmpd)[inputs]: Same.
(ghc-concurrent-output)[inputs]: Remove ghc-stm.
* gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text.
* gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-04 17:41:08 +02:00
Ricardo Wurmus c7b1d06024
gnu: pigx-rnaseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
 2019-07-04 12:42:38 +02:00
Ricardo Wurmus 5b86bcfa68
gnu: r-phangorn: Update to 2.5.5. 
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
 2019-06-29 01:34:43 +02:00
Ricardo Wurmus 7f17e60ab7
gnu: r-tximport: Update to 1.12.3. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
 2019-06-29 01:34:43 +02:00
Ricardo Wurmus dafd290d21
gnu: r-genomicfeatures: Update to 1.36.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
 2019-06-29 01:34:43 +02:00
Ricardo Wurmus c40bba2b36
gnu: r-genomicalignments: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
 2019-06-29 01:34:43 +02:00
Ricardo Wurmus 888085c36c
gnu: r-biomart: Update to 2.40.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
 2019-06-29 01:34:43 +02:00
Ricardo Wurmus f0c244229a
gnu: r-edger: Update to 3.26.5. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
 2019-06-29 01:34:43 +02:00
Ricardo Wurmus 0253b5d881
gnu: r-systempiper: Update to 1.18.2. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
 2019-06-29 01:34:42 +02:00
Ricardo Wurmus bae0f8af21
gnu: pigx-scrnaseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
 2019-06-27 23:23:29 +02:00
Ricardo Wurmus b556abe416
gnu: khmer: Update to 3.0.0a3. 
* gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3.
[source]: Remove patch; remove seqan in snippet.
[inputs]: Add seqan-1.
* gnu/packages/patches/khmer-use-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2019-06-21 11:41:54 +02:00
Ricardo Wurmus 28618b05f0
gnu: pigx-rnaseq: Update to 0.0.7. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7.
[inputs]: Add coreutils and sed.
 2019-06-20 22:29:43 +02:00
Ricardo Wurmus 30adfd3600
gnu: ngs-sdk: Update to 2.9.6. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
 2019-06-20 14:33:57 +02:00
Ricardo Wurmus 20874b7044
gnu: sra-tools: Update to 2.9.6. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
 2019-06-20 14:33:57 +02:00
Ricardo Wurmus 7cb44fb571
gnu: ncbi-vdb: Update to 2.9.6. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6.
[arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
 2019-06-20 14:33:57 +02:00
Ricardo Wurmus a6f2ced34b
gnu: Add tbsp. 
* gnu/packages/bioinformatics.scm (tbsp): New variable.
 2019-06-17 20:22:38 +02:00
Ricardo Wurmus 42df44f645
gnu: r-seurat: Update to 3.0.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
 2019-06-17 04:55:03 +02:00
Ricardo Wurmus 6dc3c58728
gnu: r-tximport: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
 2019-06-17 04:54:56 +02:00
Ricardo Wurmus 7bbd06ed59
gnu: r-systempiper: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1.
 2019-06-17 04:54:51 +02:00
Ricardo Wurmus bc70516bba
gnu: Remove r-loomr. 
The loomR package is actually non-free software according to its author.  See
https://github.com/mojaveazure/loomR/pull/24.

* gnu/packages/bioinformatics.scm (r-loomr): Remove variable.
 2019-06-14 17:32:04 +02:00
Ricardo Wurmus 6054c823ae
gnu: pigx-rnaseq: Update to 0.0.6. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.6.
[inputs]: Remove bedtools.
 2019-06-12 13:12:00 +02:00
Ricardo Wurmus 944cb87a33
gnu: Add r-psiplot. 
* gnu/packages/bioinformatics.scm (r-psiplot): New variable.
 2019-06-11 13:39:50 +02:00
Ricardo Wurmus 823e23fffe
gnu: r-msnbase: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.1.
 2019-06-09 15:19:58 +02:00
Ricardo Wurmus 85e067161a
gnu: r-iranges: Update to 2.18.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.1.
 2019-06-09 15:19:58 +02:00
Ricardo Wurmus f53b4a6b77
gnu: r-biocviews: Update to 1.52.2. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.2.
[propagated-inputs]: Add r-biocmanager.
 2019-06-01 23:04:26 +02:00
Ricardo Wurmus add5ecfd68
gnu: r-biocviews: Update to 1.52.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.1.
 2019-05-30 13:41:10 +02:00
Ricardo Wurmus d37ba98409
gnu: r-scran: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.1.
 2019-05-29 00:02:42 +02:00
Ricardo Wurmus 55cd48508e
gnu: r-scater: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.2.
 2019-05-29 00:02:37 +02:00
Ricardo Wurmus 102cf9a1ca
gnu: r-sva: Update to 3.32.1. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.1.
 2019-05-29 00:02:31 +02:00
Ricardo Wurmus 24f46e6e9e
gnu: r-genomicfeatures: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.1.
 2019-05-29 00:02:25 +02:00
Ricardo Wurmus 4eea449aaa
gnu: r-edger: Update to 3.26.4. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.4.
 2019-05-29 00:02:17 +02:00
Ricardo Wurmus 4929a30f69
gnu: r-variantannotation: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
 2019-05-29 00:02:10 +02:00
Ricardo Wurmus 164cb4da63
gnu: pigx-chipseq: Update to 0.0.41. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.41.
 2019-05-26 10:56:52 +02:00
Marius Bakke 9d0c291e3e
gnu: Move Sphinx and friends to (gnu packages sphinx). 
* gnu/packages/python-xyz.scm (python-sphinxcontrib-websupport,
python2-sphinxcontrib-websupport, python-sphinx, python2-sphinx,
python-sphinx-gallery, python2-sphinx-gallery, python-sphinx-rtd-theme,
python2-sphinx-rtd-theme, python-guzzle-sphinx-theme,
python2-guzzle-sphinx-theme, python-sphinxcontrib-newsfeed,
python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput,
python-sphinx-repoze-interface, python2-sphinx-repoze-interface,
python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme,
python-sphinx-alabaster-theme, python2-sphinx-alabaster-theme,
python-sphinx-me, python-sphinxcontrib-svg2pdfconverter): Move to ...
(gnu):
* gnu/packages/sphinx.scm: ... here.  New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
* gnu/packages/admin.scm, gnu/packages/bioinformatics.scm,
gnu/packages/calendar.scm, gnu/packages/cluster.scm,
gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/disk.scm,
gnu/packages/django.scm, gnu/packages/elf.scm, gnu/packages/emacs-xyz.scm,
gnu/packages/emulators.scm, gnu/packages/finance.scm, gnu/packages/image.scm,
gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm,
gnu/packages/openstack.scm, gnu/packages/pdf.scm, gnu/packages/python-web.scm,
gnu/packages/search.scm, gnu/packages/statistics.scm,
gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm,
gnu/packages/tls.scm, gnu/packages/web.scm: Adjust module imports.
 2019-05-24 21:54:31 +02:00
Ricardo Wurmus a9150d4c23
gnu: salmon: Update to 0.13.1. 
* gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1.
[arguments]: Adjust "do-not-look-for-boost" build phase; adjust
"prepare-rapmap" phase; adjust "use-system-libraries" phase.
[inputs]: Remove bwa, jellyfish, spdlog-for-salmon.
[native-inputs]: Add pkg-config.
(spdlog-for-salmon, bwa-for-salmon): Remove variables.
 2019-05-23 16:32:21 +02:00
Vagrant Cascadian bf70490223
gnu: umi-tools: Fix typo "containing". 
* gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
 2019-05-22 18:09:35 -07:00
Vagrant Cascadian df5fb3ca28
gnu: r-gage: Fix typo "functions". 
* gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
 2019-05-22 18:09:32 -07:00
Ricardo Wurmus a8a465e816
gnu: r-limma: Update to 3.40.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.2.
 2019-05-20 15:06:07 +02:00
Ricardo Wurmus 9c714b9ba9
gnu: r-edger: Update to 3.26.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.3.
 2019-05-20 15:06:01 +02:00
Ricardo Wurmus 7a94438130
gnu: r-scater: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.1.
 2019-05-20 12:00:38 +02:00
Ricardo Wurmus 461fb28ac5
gnu: r-seurat: Update to 3.0.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.1.
 2019-05-20 12:00:37 +02:00
Ricardo Wurmus d94c698a13
gnu: r-maldiquant: Update to 1.19.3. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.3.
 2019-05-20 12:00:37 +02:00
Ricardo Wurmus 7c97f45700
gnu: r-edger: Update to 3.26.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.1.
 2019-05-20 12:00:37 +02:00
Ricardo Wurmus a4ff3255d4
gnu: star: Update to 2.7.1a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.1a.
 2019-05-16 13:45:23 +02:00
Ricardo Wurmus 44323e63a3
gnu: Add ataqv. 
* gnu/packages/bioinformatics.scm (ataqv): New variable.
 2019-05-14 16:15:19 +02:00
Ricardo Wurmus 21ec924868
gnu: r-hdf5array: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.1.
 2019-05-11 12:05:35 +02:00
Ricardo Wurmus 3addf736d5
gnu: r-systempiper: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.0.
[propagated-inputs]: Replace r-batchjobs with r-batchtools; add r-yaml.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 9bcbca135b
gnu: r-rsamtools: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.0.
[propagated-inputs]: Add r-rhtslib.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 82d9340b0c
gnu: r-impute: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.58.0.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 2b4ac1d77e
gnu: r-rcas: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.0.
[propagated-inputs]: Add ghc-pandoc.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus 8322c860f9
gnu: r-methylkit: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.10.0.
[propagated-inputs]: Add r-mgcv.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus b173dbe617
gnu: r-annotationhub: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.0.
[propagated-inputs]: Add r-biocfilecache, r-dplyr, and r-rappdirs.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus a8abc8dd3a
gnu: r-fastseg: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.30.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus e699e8e599
gnu: r-keggrest: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus c798455d87
gnu: r-gage: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.34.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus d4ef1d59cc
gnu: r-genomicfiles: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.20.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus 70a3e4499d
gnu: r-complexheatmap: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.0.0.
[propagated-inputs]: Add r-clue and r-png.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus e2cb23404c
gnu: r-dirichletmultinomial: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.26.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 0af6efa3c5
gnu: r-ensembldb: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 96f98c5b72
gnu: r-organismdbi: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.26.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus a98c3b4ae4
gnu: r-biovizbase: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.32.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus d38fbacad1
gnu: r-ggbio: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.32.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 623be1a443
gnu: r-gqtlbase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.16.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus ed7de45655
gnu: r-snpstats: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.34.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 3c5f5b4154
gnu: r-erma: Update to 1.0.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.0.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 89ba9a7226
gnu: r-ldblock: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus a349d57a46
gnu: r-gqtlstats: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.16.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 105d9e2cb4
gnu: r-gviz: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 1b454f9f69
gnu: r-gwascat: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.0.
[propagated-inputs]: Remove r-annotationhub, r-ggbio, r-ggplot2, r-gqtlstats,
r-graph, r-gviz, r-snpstats, r-summarizedexperiment, and r-variantannotation.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 256609eb46
gnu: r-sushi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.22.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 7705165882
gnu: r-fithic: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.10.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus e998a26e1d
gnu: r-hitc: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.28.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 65925573be
gnu: r-hdf5array: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus d5625b3a9e
gnu: r-rhdf5lib: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 583b4fd6e3
gnu: r-beachmat: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.0.0.
[inputs]: Remove hdf5 and zlib.
[propagated-inputs]: Rmeove r-hdf5array, r-rcpp, r-rhdf5, and r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 029cefdd90
gnu: r-singlecellexperiment: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.6.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 70d04dc183
gnu: r-scater: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.0.
[propagated-inputs]: Add r-biocneighbors and r-biocsingular; remove r-plyr,
r-reshape2, and r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 4540727a21
gnu: r-scran: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.0.
[propagated-inputs]: Add r-bh, r-biocsingular, and r-dqrng; remove r-rhdf5lib.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus f2a63d1588
gnu: r-delayedmatrixstats: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus fab5f7c8d9
gnu: r-interactivedisplaybase: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.22.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus 975b72fa10
gnu: r-edaseq: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.18.0.
 2019-05-06 00:14:39 +02:00