From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47826) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dhy5G-0004fG-QQ for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dhy5D-0003kH-E8 for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:06 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:59929) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dhy5D-0003k6-BE for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dhy5D-0004t5-5p for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:03 -0400 Subject: [bug#28109] [PATCH 03/10] gnu: Add r-fastseg. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 16 Aug 2017 15:08:52 +0200 Message-Id: <20170816130859.15069-3-rekado@elephly.net> In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 28109@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (r-fastseg): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3571cb96c..4207b2a9d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9287,6 +9287,36 @@ modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.") (license license:artistic2.0))) +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.13.3