From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] htsjdk: Use ant-build-system. Date: Mon, 14 Mar 2016 13:04:23 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48777) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1afREi-0006QG-CV for guix-devel@gnu.org; Mon, 14 Mar 2016 08:04:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1afREf-0004Td-4u for guix-devel@gnu.org; Mon, 14 Mar 2016 08:04:36 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:55256) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1afREe-0004TO-P9 for guix-devel@gnu.org; Mon, 14 Mar 2016 08:04:33 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 57347380EAA for ; Mon, 14 Mar 2016 13:04:31 +0100 (CET) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 7vdShiLekckU for ; Mon, 14 Mar 2016 13:04:25 +0100 (CET) Received: from HTCATWO.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 pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Mon, 14 Mar 2016 13:04:25 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-htsjdk-Use-ant-build-system.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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel >From 25285f8516a3129230357cf4edec2d47c8ab89c4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 14 Mar 2016 13:02:48 +0100 Subject: [PATCH] gnu: htsjdk: Use ant-build-system. * gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use ant-build-system. [arguments]: Adapt for ant-build-system. --- gnu/packages/bioinformatics.scm | 28 +++++++++++----------------- 1 file changed, 11 insertions(+), 17 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ed2b634..5dedf10 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -26,6 +26,7 @@ #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system perl) @@ -2052,24 +2053,17 @@ from high-throughput sequencing assays.") (snippet '(substitute* "build.xml" (("failifexecutionfails=\"true\"") "failifexecutionfails=\"false\""))))) - (build-system gnu-build-system) + (build-system ant-build-system) (arguments - `(#:modules ((srfi srfi-1) - (guix build gnu-build-system) - (guix build utils)) - #:phases (alist-replace - 'build - (lambda _ - (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk")) - (zero? (system* "ant" "all" - (string-append "-Ddist=" - (assoc-ref %outputs "out") - "/share/java/htsjdk/")))) - (fold alist-delete %standard-phases - '(configure install check))))) - (native-inputs - `(("ant" ,ant) - ("jdk" ,icedtea "jdk"))) + `(#:tests? #f ; test require Internet access + #:make-flags + (list (string-append "-Ddist=" (assoc-ref %outputs "out") + "/share/java/htsjdk/")) + #:build-target "all" + #:phases + (modify-phases %standard-phases + ;; The build phase also installs the jars + (delete 'install)))) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description -- 2.1.0