From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add libBigWig. Date: Wed, 24 Feb 2016 17:21:47 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37809) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aYcCP-0008UL-Jw for guix-devel@gnu.org; Wed, 24 Feb 2016 11:22:02 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aYcCJ-0002sP-Gr for guix-devel@gnu.org; Wed, 24 Feb 2016 11:22:01 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:48051) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aYcCJ-0002rf-3m for guix-devel@gnu.org; Wed, 24 Feb 2016 11:21:55 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 97ECD380925 for ; Wed, 24 Feb 2016 17:21:53 +0100 (CET) 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 B_qOerBRJ-aE for ; Wed, 24 Feb 2016 17:21:48 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Wed, 24 Feb 2016 17:21:48 +0100 (CET) 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 --=-=-= Content-Type: text/plain Hi Guix, the description is a little short. Basically, this is a cleaner reimplementation of a popular tool/library that is released under a non-commercial license. There is little more I can say about it and the original description just references that other tool. Any ideas how to improve this? ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-libBigWig.patch" >From d315b3857072fdb0f2f322eaa7562d0bf0c92017 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 24 Feb 2016 17:17:53 +0100 Subject: [PATCH] gnu: Add libBigWig. * gnu/packages/bioinformatics.scm (libbigwig): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 623eeb6..16cda70 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages curl) #:use-module (gnu packages file) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) @@ -1081,6 +1082,50 @@ preparation protocols.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public libbigwig + (package + (name "libbigwig") + (version "0.1.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/dpryan79/libBigWig/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list "CC=gcc" + (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'check 'disable-curl-test + (lambda _ + (substitute* "Makefile" + (("./test/testRemote.*") "")) + #t)) + (add-before 'install 'create-target-dirs + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/lib")) + (mkdir-p (string-append out "/include")) + #t)))))) + (inputs + `(("zlib" ,zlib) + ("curl" ,curl))) + (native-inputs + `(("doxygen" ,doxygen))) + (home-page "https://github.com/dpryan79/libBigWig") + (synopsis "C library for handling bigWig files") + (description + "This package provides a C library for parsing local and remote BigWig +files.") + (license license:expat))) + (define-public deeptools (package (name "deeptools") -- 2.1.0 --=-=-=--