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2073 Commits

Author SHA1 Message Date
Efraim Flashner
d371112bd0
gnu: edirect: Update to 12.1.20190819. 
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190819.
 2019-08-20 11:08:42 +03:00
Ricardo Wurmus
a6a19fb14c
gnu: r-gviz: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.1.
 2019-08-19 16:25:33 +02:00
Ricardo Wurmus
b65bd33c36
gnu: r-edger: Update to 3.26.7. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.7.
 2019-08-16 22:41:27 +02:00
Marius Bakke
462ad9f56b
Merge branch 'master' into core-updates 2019-08-13 20:42:06 +02:00
Ricardo Wurmus
c2847323d8
gnu: freebayes: Simplify and enable tests. 
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set
make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles"
phase; move build of tabixpp and vcflib to separate phase
"build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build"
phase.
 2019-08-09 12:15:26 +02:00
Ricardo Wurmus
7cd98e868e
gnu: freebayes: Move bamtools to inputs. 
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools
from here...
[inputs]: ...to here.
 2019-08-09 12:15:26 +02:00
Pierre Neidhardt
8803dbdad8
gnu: Add freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): New variable.
 2019-08-09 10:47:25 +03:00
Pierre Neidhardt
95fb1a1851
gnu: Add vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): New variable.
(tabixpp-freebayes): New private variable.
 2019-08-09 10:43:40 +03:00
Ricardo Wurmus
90060e2071
gnu: r-hdf5array: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
 2019-08-08 16:47:05 +02:00
Ricardo Wurmus
a39f2e4cea
gnu: r-biocparallel: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
 2019-08-08 16:47:02 +02:00
Efraim Flashner
1a069a170c
Revert "gnu: Add vcflib." 
This reverts commit 194e45f90a.

This commit does not have a good commit message, and it breaks master
 2019-08-08 15:34:05 +03:00
Efraim Flashner
6bc63fd8a7
Revert "gnu: Add freebayes." 
This reverts commit 173e046950.
 2019-08-08 15:32:51 +03:00
Pierre Neidhardt
173e046950
gnu: Add freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): New variable.
 2019-08-08 15:18:34 +03:00
Pierre Neidhardt
194e45f90a
gnu: Add vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): New variable.
 2019-08-08 15:18:33 +03:00
Pierre Neidhardt
7d71557d4d
gnu: Add fastahack. 
* gnu/packages/bioinformatics.scm (fastahack): New variable.
 2019-08-08 15:18:32 +03:00
Pierre Neidhardt
70782dddff
gnu: Add fsom. 
* gnu/packages/bioinformatics.scm (fsom): New variable.
 2019-08-08 15:18:31 +03:00
Pierre Neidhardt
8cd51276e5
gnu: Add multichoose. 
* gnu/packages/bioinformatics.scm (multichoose): New variable.
 2019-08-08 15:18:30 +03:00
Pierre Neidhardt
7faa70cf2b
gnu: Add smithwaterman. 
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
 2019-08-08 15:18:29 +03:00
Pierre Neidhardt
62a031afc4
gnu: Add tabixpp. 
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
 2019-08-08 15:18:14 +03:00
Robert Vollmert
a1eb8be8ca
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>
 2019-08-07 22:05:29 -04:00
Ricardo Wurmus
c8e141ab02
gnu: r-msnid: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus
afe4be49f1
gnu: r-rcas: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
 2019-08-06 15:49:00 +02:00
Ricardo Wurmus
76d9b08e1b
gnu: r-genomicfeatures: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus
e16fe0b50a
gnu: r-rtracklayer: Update to 1.44.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus
6f8760d9f8
gnu: r-summarizedexperiment: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus
2ebd2b440d
gnu: r-biomart: Update to 2.40.3. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
 2019-08-06 15:48:59 +02:00
Ricardo Wurmus
fbd761fe9b
gnu: r-limma: Update to 3.40.6. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
 2019-08-06 15:48:59 +02:00
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