From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: [PATCH] gnu: Add r-variantannotation. Date: Wed, 30 Mar 2016 15:16:42 +0200 Message-ID: <87oa9wrtqd.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50397) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1alFz2-0002mq-U2 for guix-devel@gnu.org; Wed, 30 Mar 2016 09:16:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1alFyz-0007LU-NW for guix-devel@gnu.org; Wed, 30 Mar 2016 09:16:28 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:60652) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1alFyz-0007LP-JQ for guix-devel@gnu.org; Wed, 30 Mar 2016 09:16:25 -0400 Received: from [143.121.239.252] (port=24434 helo=roel-tp) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1alFyz-0003kh-33 for guix-devel@gnu.org; Wed, 30 Mar 2016 09:16:25 -0400 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-Add-r-variantannotation.patch >From b973ee57f42e1e094d3dc377a5175de6ed252bc4 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 30 Mar 2016 15:03:56 +0200 Subject: [PATCH 1/2] gnu: Add r-variantannotation. * gnu/packages/bioinformatics.scm (r-variantannotation): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 887f6cc..79990a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4040,6 +4040,38 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-variantannotation + (package + (name "r-variantannotation") + (version "1.16.4") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "VariantAnnotation" version)) + (sha256 + (base32 + "1z42j3p9b8h725inq8n0230llsdbav3gwcxy1nliypzfkxbzahsb")))) + (properties + `((upstream-name . "VariantAnnotation"))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-bsgenome" ,r-bsgenome) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rsamtools" ,r-rsamtools) + ("r-zlibbioc" ,r-zlibbioc))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/VariantAnnotation") + (synopsis "Package for annotation of genetic variants") + (description "This R package can annotate variants, compute amino acid +coding changes and predict coding outcomes.") + (license license:artistic2.0))) + (define-public r-xvector (package (name "r-xvector") -- 2.5.5 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0002-gnu-Add-r-zlibbioc.patch >From 38099e08370f84d589cdc7a486807c44f160949e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 30 Mar 2016 15:05:31 +0200 Subject: [PATCH 2/2] gnu: Add r-zlibbioc. * gnu/packages/bioinformatics.scm (r-zlibbioc): New variable. --- gnu/packages/bioinformatics.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79990a4..5f3d5d5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4777,6 +4777,25 @@ identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) +(define-public r-zlibbioc + (package + (name "r-zlibbioc") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "zlibbioc" version)) + (sha256 + (base32 + "01wc26ndg4jsn1wyrl6zzq636gxaip5fci0xapym4lh9wryc4wnw")))) + (properties + `((upstream-name . "zlibbioc"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/zlibbioc") + (synopsis "Provider for zlib-1.2.5 to R packages") + (description "This package uses the source code of zlib-1.2.5 to create +libraries for systems that do not have these available via other means.") + (license license:artistic2.0))) + (define-public pepr (package (name "pepr") -- 2.5.5 --=-=-= Content-Type: text/plain Dear Guix, I want to add another R package: VariantAnnotation. For this I also had to add another R package called "zlibbioc". Even though we provide zlib in GNU Guix, and it also uses the zlib input instead of zlib provided by this package, it is a required dependency of VariantAnnotation. Instead of customizing the VariantAnnotation package (and deviate from upstream development), I believe this is a fairly nice solution. I hope this is fine with you. Kind regards, Roel Janssen --=-=-=--