From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add Piranha. Date: Tue, 26 Apr 2016 16:09:41 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:51653) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1av3gb-0006ok-Ps for guix-devel@gnu.org; Tue, 26 Apr 2016 10:10:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1av3gW-0000TI-QB for guix-devel@gnu.org; Tue, 26 Apr 2016 10:09:57 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:48435) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1av3gW-0000T9-Cn for guix-devel@gnu.org; Tue, 26 Apr 2016 10:09:52 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id E309B380411 for ; Tue, 26 Apr 2016 16:09:50 +0200 (CEST) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id HL2_3RxPy92n for ; Tue, 26 Apr 2016 16:09:45 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Tue, 26 Apr 2016 16:09:45 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-Piranha.patch" 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" To: "guix-devel@gnu.org" >From 8ebcd50666e13407d2b74907c9bc5e37ee420192 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 26 Apr 2016 16:08:47 +0200 Subject: [PATCH] gnu: Add Piranha. * gnu/packages/bioinformatics.scm (piranha): New variable. --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35c3334..7a93c72 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5209,6 +5209,68 @@ two-dimensional genome scans.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public piranha + (package + (name "piranha") + (version "1.1.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/smithlabcode/piranha" + "/archive/svn/tags/piranha-" + version ".tar.gz")) + (sha256 + (base32 + "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'copy-smithlab-cpp + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "src/smithlab_cpp") + (for-each (lambda (file) + (copy-file file + (string-append "./src/smithlab_cpp/" + (basename file)))) + (find-files (assoc-ref inputs "smithlab-cpp"))) + #t)) + (add-after 'install 'install-to-store + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*"))) + #t))) + #:configure-flags + (list (string-append "--with-bam_tools_headers=" + (assoc-ref %build-inputs "bamtools") "/include/bamtools") + (string-append "--with-bam_tools_library=" + (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) + (inputs + `(("bamtools" ,bamtools) + ("samtools" ,samtools-0.1) + ("gsl" ,gsl) + ("smithlab-cpp" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit "3723e2d"))) + (file-name "smithlab_cpp-3723e2d-checkout") + (sha256 + (base32 + "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))) + (native-inputs + `(("python" ,python-2))) + (home-page "https://github.com/smithlabcode/piranha") + (synopsis "Peak-caller for CLIP-seq and RIP-seq data") + (description + "Piranha is a peak-caller for CLIP-seq and RIP-seq data.") + (license license:gpl3+))) + (define-public pepr (package (name "pepr") -- 2.7.3