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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47171@debbugs.gnu.org Cc: zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161583177218434 (code B ref 47171); Mon, 15 Mar 2021 18:10:04 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:32 +0000 Received: from localhost ([127.0.0.1]:36953 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrel-0004n9-Br for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:31 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:46936) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLref-0004lX-Qq for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:26 -0400 Received: by mail-wr1-f53.google.com with SMTP id v4so6158300wrp.13 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:25 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=ZiOyeAbP8hVWcFWNzy1l+NEXiwferumVNSVS7JSIH8g=; b=N73aXrAV2+UySs3nKF4Y387VCfwYiyrFmPNf8jUkhHdrNj96Ve381xc41pU1VOxNSs 1KGl//1BxeWKUaSH7ePIb43ubaXJnqWj0ufOBzyHBOS6rRNsJ74FfTfOxvGBobvprerd rlEoqgHaGDfViX71Bh8y7CiCFhLmaQAbMcywkI1YdycsEeBcIhLh42mBZGTLHCZYaLOz lL7Q8WONqUIc1ef/lapiLDjPtDVsNVUalWmeZ417BO3tsrJPtN4sYPOYZPRgpFgpZ4HZ IwY0tmz5Ln4YbdT0H7/Bwd3pFMwllWp32KJKweUx2tKQwJ7dcHSfsvOMntv5FQB/t216 fJFw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=ZiOyeAbP8hVWcFWNzy1l+NEXiwferumVNSVS7JSIH8g=; b=Q2/KbwFvrkFdzSJcuzxRc8nkTokWIqbgvSXuiRMjkb3mkjMbl/VIpucuRtG5cH2gyq kClpVO6p76+h2zRpXviBDLSL7nQx9HXYG/DqcdDTJsoHHUq+dd+fAWeoXoziUNrRMDjq 4ipus4ve/tk4ywoRmri/mvb4z/PQfmR2tXd/P5W7PqoLiMl7eJhSbitWYSFBOssoZ6f9 N2EsY/pPGBXyIHL+/uDeAHUp3PMAdt5OcpYNCbC4w4hZu7BubB+lxi07dPri3FvfYLam 76xviKAojImVL+VLAz1axj3aCN8COZJyPldzWOxqG4uTnJoNOB8CwYnChIPuoCbBGqAx r8yA== X-Gm-Message-State: AOAM532qTbI0K3KnJ40be4Xei0VJwZVS+kYvxL2U9lqU2vrwrWd0jPjN 6pVUpaCsm1Sw/OAoGemYMAPz4nQt/oU= X-Google-Smtp-Source: ABdhPJys7/MNpjysS0OovD38684EHQcuLX4z+MGyTwjwGtwspP21JQ/2O5juJnwrzGgc/69kpQ8VGg== X-Received: by 2002:a5d:6b50:: with SMTP id x16mr832612wrw.379.1615831759935; Mon, 15 Mar 2021 11:09:19 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:19 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:09:00 +0100 Message-Id: <20210315180904.8346-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315180904.8346-1-zimon.toutoune@gmail.com> References: <20210315180904.8346-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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")