From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47398) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1erTO6-0002WG-JB for guix-patches@gnu.org; Thu, 01 Mar 2018 13:57:07 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1erTO2-0003kT-BM for guix-patches@gnu.org; Thu, 01 Mar 2018 13:57:06 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:60026) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1erTO2-0003kP-73 for guix-patches@gnu.org; Thu, 01 Mar 2018 13:57:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1erTO1-00030r-UO for guix-patches@gnu.org; Thu, 01 Mar 2018 13:57:01 -0500 Subject: [bug#30666] [PATCH 14/17] gnu: Add java-htsjdk-latest. Resent-Message-ID: From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:46 +0100 Message-ID: <20180301184149.27239-14-ricardo.wurmus@mdc-berlin.de> In-Reply-To: <20180301184149.27239-1-ricardo.wurmus@mdc-berlin.de> References: <20180301184149.27239-1-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: 30666@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 98c0aff3a..2402fa0e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3019,6 +3019,49 @@ sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.") (license license:expat))) +(define-public java-htsjdk-latest + (package + (name "java-htsjdk") + (version "2.14.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samtools/htsjdk.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; test require Scala + #:jdk ,icedtea-8 + #:jar-name "htsjdk.jar" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; The tests require the scalatest package. + (add-after 'unpack 'remove-tests + (lambda _ (delete-file-recursively "src/test") #t))))) + (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-junit" ,java-junit))) + (home-page "http://samtools.github.io/htsjdk/") + (synopsis "Java API for high-throughput sequencing data (HTS) formats") + (description + "HTSJDK is an implementation of a unified Java library for accessing +common file formats, such as SAM and VCF, used for high-throughput +sequencing (HTS) data. There are also an number of useful utilities for +manipulating HTS data.") + (license license:expat))) + ;; This version matches java-htsjdk 2.3.0. Later versions also require a more ;; recent version of java-htsjdk, which depends on gradle. (define-public java-picard -- 2.15.1