From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:52030) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eHTH8-0007Tk-Pq for guix-patches@gnu.org; Wed, 22 Nov 2017 06:33:07 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eHTH4-0003ah-QA for guix-patches@gnu.org; Wed, 22 Nov 2017 06:33:06 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:43238) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1eHTH4-0003aZ-Ld for guix-patches@gnu.org; Wed, 22 Nov 2017 06:33:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1eHTH4-0007vi-G4 for guix-patches@gnu.org; Wed, 22 Nov 2017 06:33:02 -0500 Subject: [bug#29394] [PATCH 05/12] gnu: java-htsjdk: Update to 2.3.0. Resent-Message-ID: From: Date: Wed, 22 Nov 2017 12:30:35 +0100 Message-ID: <20171122113042.1734-5-ricardo.wurmus@mdc-berlin.de> In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain 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: 29394@debbugs.gnu.org Cc: Ricardo Wurmus From: Ricardo Wurmus * gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0. [arguments]: Build with JDK 8. [inputs]: Add java-ngs, java-snappy, java-commons-compress, java-commons-logging-minimal, java-commons-jexl-2, and java-xz. [native-inputs]: Add java-testng. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8d7361ff..6c71d7362 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2961,7 +2961,7 @@ from high-throughput sequencing assays.") (define-public java-htsjdk (package (name "java-htsjdk") - (version "1.129") + (version "2.3.0") ; last version without build dependency on gradle (source (origin (method url-fetch) (uri (string-append @@ -2970,15 +2970,18 @@ from high-throughput sequencing assays.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) + "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq")) (modules '((guix build utils))) - ;; remove build dependency on git - (snippet '(substitute* "build.xml" - (("failifexecutionfails=\"true\"") - "failifexecutionfails=\"false\""))))) + (snippet + ;; Delete pre-built binaries + '(begin + (delete-file-recursively "lib") + (mkdir-p "lib") + #t)))) (build-system ant-build-system) (arguments `(#:tests? #f ; test require Internet access + #:jdk ,icedtea-8 #:make-flags (list (string-append "-Ddist=" (assoc-ref %outputs "out") "/share/java/htsjdk/")) @@ -2987,6 +2990,15 @@ from high-throughput sequencing assays.") (modify-phases %standard-phases ;; The build phase also installs the jars (delete 'install)))) + (inputs + `(("java-ngs" ,java-ngs) + ("java-snappy-1" ,java-snappy-1) + ("java-commons-compress" ,java-commons-compress) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-xz" ,java-xz))) + (native-inputs + `(("java-testng" ,java-testng))) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description -- 2.14.1