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dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=dEFYgRnF; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 3E12A1A2DA X-Spam-Score: 2.66 X-Migadu-Scanner: scn0.migadu.com X-TUID: nWYz+Y7ytwQO * gnu/packages/bioinformatics.scm (r-ensembldb): Move from here... * gnu/packages/bioconductor.scm (r-ensembldb): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ 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 7439ad96da..7e86af7d21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2398,6 +2398,51 @@ 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 e6692ece0c..baef88cd2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,51 +8934,6 @@ 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")) -- 2.30.1