| Age | Commit message (Expand) | Author |
|---|
| 2019-08-09 | 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.
| Ricardo Wurmus |
| 2019-08-09 | gnu: freebayes: Move bamtools to inputs....* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools
from here...
[inputs]: ...to here.
| Ricardo Wurmus |
| 2019-08-09 | gnu: Add freebayes....* gnu/packages/bioinformatics.scm (freebayes): New variable.
| Pierre Neidhardt |
| 2019-08-09 | gnu: Add vcflib....* gnu/packages/bioinformatics.scm (vcflib): New variable.
(tabixpp-freebayes): New private variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: r-hdf5array: Update to 1.12.2....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
| Ricardo Wurmus |
| 2019-08-08 | gnu: r-biocparallel: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
| Ricardo Wurmus |
| 2019-08-08 | Revert "gnu: Add vcflib."...This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b.
This commit does not have a good commit message, and it breaks master
| Efraim Flashner |
| 2019-08-08 | Revert "gnu: Add freebayes."...This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.
| Efraim Flashner |
| 2019-08-08 | gnu: Add freebayes....* gnu/packages/bioinformatics.scm (freebayes): New variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: Add vcflib....* gnu/packages/bioinformatics.scm (vcflib): New variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: Add fastahack....* gnu/packages/bioinformatics.scm (fastahack): New variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: Add fsom....* gnu/packages/bioinformatics.scm (fsom): New variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: Add multichoose....* gnu/packages/bioinformatics.scm (multichoose): New variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: Add smithwaterman....* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
| Pierre Neidhardt |
| 2019-08-08 | gnu: Add tabixpp....* gnu/packages/bioinformatics.scm (tabixpp): New variable.
| Pierre Neidhardt |
| 2019-08-07 | 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>
| Robert Vollmert |
| 2019-08-06 | gnu: r-msnid: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-rcas: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-genomicfeatures: Update to 1.36.4....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-rtracklayer: Update to 1.44.2....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-summarizedexperiment: Update to 1.14.1....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-biomart: Update to 2.40.3....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-limma: Update to 3.40.6....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
| Ricardo Wurmus |
| 2019-08-06 | gnu: r-edger: Update to 3.26.6....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
| Ricardo Wurmus |
| 2019-08-05 | 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>
| Brian Leung |
| 2019-07-25 | 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.
| Ludovic Courtès |
| 2019-07-22 | 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.
| Ricardo Wurmus |
| 2019-07-15 | gnu: Add python-ont-fast5-api....* gnu/packages/bioinformatics.scm (python-ont-fast5-api): New variable.
| Ricardo Wurmus |
| 2019-07-13 | gnu: pigx-rnaseq: Update to 0.0.10....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.10.
| Ricardo Wurmus |
| 2019-07-09 | gnu: r-biocinstaller: Remove entirely....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.
| Tobias Geerinckx-Rice |
| 2019-07-08 | 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.
| Tobias Geerinckx-Rice |
| 2019-07-08 | 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.
| Tobias Geerinckx-Rice |
| 2019-07-05 | gnu: nanopolish: Update to 0.11.1-1.6331dc4....* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
| Ricardo Wurmus |
| 2019-07-04 | gnu: pigx-rnaseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-phangorn: Update to 2.5.5....* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-tximport: Update to 1.12.3....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-genomicfeatures: Update to 1.36.3....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-genomicalignments: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-biomart: Update to 2.40.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-edger: Update to 3.26.5....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-systempiper: Update to 1.18.2....* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
| Ricardo Wurmus |
| 2019-06-27 | gnu: pigx-scrnaseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
| Ricardo Wurmus |
| 2019-06-21 | 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.
| Ricardo Wurmus |
| 2019-06-20 | gnu: pigx-rnaseq: Update to 0.0.7....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7.
[inputs]: Add coreutils and sed.
| Ricardo Wurmus |
| 2019-06-20 | gnu: ngs-sdk: Update to 2.9.6....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
| Ricardo Wurmus |
| 2019-06-20 | gnu: sra-tools: Update to 2.9.6....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
| Ricardo Wurmus |
| 2019-06-20 | 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".
| Ricardo Wurmus |
| 2019-06-17 | gnu: Add tbsp....* gnu/packages/bioinformatics.scm (tbsp): New variable.
| Ricardo Wurmus |
| 2019-06-17 | gnu: r-seurat: Update to 3.0.2....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
| Ricardo Wurmus |
| 2019-06-17 | gnu: r-tximport: Update to 1.12.1....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
| Ricardo Wurmus |
