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author | zimoun <zimon.toutoune@gmail.com> | 2021-05-21 22:26:04 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2021-05-31 15:37:59 +0200 |
commit | 88cf24febb43768c780d55cd496034d227096550 (patch) | |
tree | 8fb1aae94c1af0d3d72d9536be1962763d905fb5 /gnu | |
parent | fea33b9d1e35c18fb214c12653b7624a627271d9 (diff) | |
download | guix-patches-88cf24febb43768c780d55cd496034d227096550.tar guix-patches-88cf24febb43768c780d55cd496034d227096550.tar.gz |
gnu: r-ensembldb: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioconductor.scm | 45 | ||||
-rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
2 files changed, 45 insertions, 45 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56e7186209..eb0bcb22c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2603,6 +2603,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + (define-public r-fastseg (package (name "r-fastseg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b17ca0fabd..4be61522b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,51 +9108,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-ensembldb - (package - (name "r-ensembldb") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ensembldb" version)) - (sha256 - (base32 - "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/jotsetung/ensembldb") - (synopsis "Utilities to create and use Ensembl-based annotation databases") - (description - "The package provides functions to create and use transcript-centric -annotation databases/packages. The annotation for the databases are directly -fetched from Ensembl using their Perl API. The functionality and data is -similar to that of the TxDb packages from the @code{GenomicFeatures} package, -but, in addition to retrieve all gene/transcript models and annotations from -the database, the @code{ensembldb} package also provides a filter framework -allowing to retrieve annotations for specific entries like genes encoded on a -chromosome region or transcript models of lincRNA genes.") - ;; No version specified - (license license:lgpl3+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) |