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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-Spam-Score: 2.70 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=N73aXrAV; 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: 62A5AB16D X-Spam-Score: 2.70 X-Migadu-Scanner: scn0.migadu.com X-TUID: RrxUBwDM8iyz * gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 --------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ae212dfac..897e85dfe3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1621,6 +1621,44 @@ databases. Packages produced are intended to be used with AnnotationDbi.") on Bioconductor or which replace R functions.") (license license:artistic2.0))) +(define-public r-biomart + (package + (name "r-biomart") + (version "2.46.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biomaRt" version)) + (sha256 + (base32 + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + (properties + `((upstream-name . "biomaRt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) + ("r-progress" ,r-progress) + ("r-rappdirs" ,r-rappdirs) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biomaRt") + (synopsis "Interface to BioMart databases") + (description + "biomaRt provides an interface to a growing collection of databases +implementing the @url{BioMart software suite, http://www.biomart.org}. The +package enables retrieval of large amounts of data in a uniform way without +the need to know the underlying database schemas or write complex SQL queries. +Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, +Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt +users direct access to a diverse set of data and enable a wide range of +powerful online queries from gene annotation to database mining.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a45196bc5b..289a96f572 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biomart - (package - (name "r-biomart") - (version "2.46.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biomaRt" version)) - (sha256 - (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) - (properties - `((upstream-name . "biomaRt"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/biomaRt") - (synopsis "Interface to BioMart databases") - (description - "biomaRt provides an interface to a growing collection of databases -implementing the @url{BioMart software suite, http://www.biomart.org}. The -package enables retrieval of large amounts of data in a uniform way without -the need to know the underlying database schemas or write complex SQL queries. -Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, -Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt -users direct access to a diverse set of data and enable a wide range of -powerful online queries from gene annotation to database mining.") - (license license:artistic2.0))) - (define-public r-biocparallel (package (name "r-biocparallel") -- 2.30.1