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
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
8803dbdad8
gnu: Add freebayes.
...
* gnu/packages/bioinformatics.scm (freebayes): New variable.
2019-08-09 10:47:25 +03:00
95fb1a1851
gnu: Add vcflib.
...
* gnu/packages/bioinformatics.scm (vcflib): New variable.
(tabixpp-freebayes): New private variable.
2019-08-09 10:43:40 +03:00
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
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
1a069a170c
Revert "gnu: Add vcflib."
...
This reverts commit 194e45f90a
2019-08-08 15:34:05 +03:00
6bc63fd8a7
Revert "gnu: Add freebayes."
...
This reverts commit 173e046950
2019-08-08 15:32:51 +03:00
173e046950
gnu: Add freebayes.
...
* gnu/packages/bioinformatics.scm (freebayes): New variable.
2019-08-08 15:18:34 +03:00
194e45f90a
gnu: Add vcflib.
...
* gnu/packages/bioinformatics.scm (vcflib): New variable.
2019-08-08 15:18:33 +03:00
7d71557d4d
gnu: Add fastahack.
...
* gnu/packages/bioinformatics.scm (fastahack): New variable.
2019-08-08 15:18:32 +03:00
70782dddff
gnu: Add fsom.
...
* gnu/packages/bioinformatics.scm (fsom): New variable.
2019-08-08 15:18:31 +03:00
8cd51276e5
gnu: Add multichoose.
...
* gnu/packages/bioinformatics.scm (multichoose): New variable.
2019-08-08 15:18:30 +03:00
7faa70cf2b
gnu: Add smithwaterman.
...
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
2019-08-08 15:18:29 +03:00
62a031afc4
gnu: Add tabixpp.
...
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
2019-08-08 15:18:14 +03:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
48182cff03
gnu: r-biocinstaller: Remove entirely.
...
This follows up on commit 0971f8bd88https://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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
a6f2ced34b
gnu: Add tbsp.
...
* gnu/packages/bioinformatics.scm (tbsp): New variable.
2019-06-17 20:22:38 +02:00
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
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