summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
Commit message (Collapse)AuthorAge
* gnu: edirect: Update to 12.1.20190819.Efraim Flashner2019-08-20
| | | | * gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190819.
* gnu: r-gviz: Update to 1.28.1.Ricardo Wurmus2019-08-19
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.1.
* gnu: r-edger: Update to 3.26.7.Ricardo Wurmus2019-08-16
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.7.
* gnu: freebayes: Simplify and enable tests.Ricardo Wurmus2019-08-09
| | | | | | | | * 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.
* gnu: freebayes: Move bamtools to inputs.Ricardo Wurmus2019-08-09
| | | | | | * gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools from here... [inputs]: ...to here.
* gnu: Add freebayes.Pierre Neidhardt2019-08-09
| | | | * gnu/packages/bioinformatics.scm (freebayes): New variable.
* gnu: Add vcflib.Pierre Neidhardt2019-08-09
| | | | | * gnu/packages/bioinformatics.scm (vcflib): New variable. (tabixpp-freebayes): New private variable.
* gnu: r-hdf5array: Update to 1.12.2.Ricardo Wurmus2019-08-08
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
* gnu: r-biocparallel: Update to 1.18.1.Ricardo Wurmus2019-08-08
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
* Revert "gnu: Add vcflib."Efraim Flashner2019-08-08
| | | | | | This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b. This commit does not have a good commit message, and it breaks master
* Revert "gnu: Add freebayes."Efraim Flashner2019-08-08
| | | | This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.
* gnu: Add freebayes.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (freebayes): New variable.
* gnu: Add vcflib.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (vcflib): New variable.
* gnu: Add fastahack.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (fastahack): New variable.
* gnu: Add fsom.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (fsom): New variable.
* gnu: Add multichoose.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (multichoose): New variable.
* gnu: Add smithwaterman.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (smithwaterman): New variable.
* gnu: Add tabixpp.Pierre Neidhardt2019-08-08
| | | | * gnu/packages/bioinformatics.scm (tabixpp): New variable.
* gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml.Robert Vollmert2019-08-07
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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>
* gnu: r-msnid: Update to 1.18.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
* gnu: r-rcas: Update to 1.10.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
* gnu: r-genomicfeatures: Update to 1.36.4.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
* gnu: r-rtracklayer: Update to 1.44.2.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
* gnu: r-summarizedexperiment: Update to 1.14.1.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
* gnu: r-biomart: Update to 2.40.3.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
* gnu: r-limma: Update to 3.40.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
* gnu: r-edger: Update to 3.26.6.Ricardo Wurmus2019-08-06
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
* gnu: khmer: Make gzip timestamps writable.Brian Leung2019-08-05
| | | | | | | * gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase to make gzip timestamps writable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Explicitly refer to 'guile-json-1' when needed.Ludovic Courtès2019-07-25
| | | | | | | | | | | | | * 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.
* gnu: htslib: Propagate zlib.Ricardo Wurmus2019-07-22
| | | | | | | Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here.
* gnu: Add python-ont-fast5-api.Ricardo Wurmus2019-07-15
| | | | * gnu/packages/bioinformatics.scm (python-ont-fast5-api): New variable.
* gnu: pigx-rnaseq: Update to 0.0.10.Ricardo Wurmus2019-07-13
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.10.
* gnu: r-biocinstaller: Remove entirely.Tobias Geerinckx-Rice2019-07-09
| | | | | | | | This follows up on commit 0971f8bd884b6e92b77d9e12030cd58279699183, 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.
* gnu: Remove r-biocinstaller.Tobias Geerinckx-Rice2019-07-08
| | | | | | | It requires R < 3.6 and is no longer supported. * gnu/packages/bioinformatics.scm (r-biocinstaller): Define as deprecated in favour of r-biocmanager.
* gnu: r-xbioc: Update to 0.1.16-1.6ff0670.Tobias Geerinckx-Rice2019-07-08
| | | | | | | | | 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.
* gnu: nanopolish: Update to 0.11.1-1.6331dc4.Ricardo Wurmus2019-07-05
| | | | * gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
* gnu: pigx-rnaseq: Update to 0.0.8.Ricardo Wurmus2019-07-04
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
* gnu: r-phangorn: Update to 2.5.5.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
* gnu: r-tximport: Update to 1.12.3.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
* gnu: r-genomicfeatures: Update to 1.36.3.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
* gnu: r-genomicalignments: Update to 1.20.1.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
* gnu: r-biomart: Update to 2.40.1.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
* gnu: r-edger: Update to 3.26.5.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
* gnu: r-systempiper: Update to 1.18.2.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
* gnu: pigx-scrnaseq: Update to 0.0.8.Ricardo Wurmus2019-06-27
| | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
* gnu: khmer: Update to 3.0.0a3.Ricardo Wurmus2019-06-21
| | | | | | | | * 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.
* gnu: pigx-rnaseq: Update to 0.0.7.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed.
* gnu: ngs-sdk: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
* gnu: sra-tools: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
* gnu: ncbi-vdb: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".