From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:43064) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1erTHJ-00010m-AC for guix-patches@gnu.org; Thu, 01 Mar 2018 13:50:06 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1erTHG-0006nu-Pc for guix-patches@gnu.org; Thu, 01 Mar 2018 13:50:05 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:59969) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1erTHG-0006ne-LC for guix-patches@gnu.org; Thu, 01 Mar 2018 13:50:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1erTHG-0002nG-BC for guix-patches@gnu.org; Thu, 01 Mar 2018 13:50:02 -0500 Subject: [bug#30666] [PATCH 05/17] gnu: Add java-biojava-core. Resent-Message-ID: From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:37 +0100 Message-ID: <20180301184149.27239-5-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-biojava-core): New variable. --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c427a6d03..60dbc956a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11886,3 +11886,59 @@ variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) + +(define-public java-biojava-core + (package + (name "java-biojava-core") + (version "4.2.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biojava/biojava") + (commit (string-append "biojava-" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk")))) + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-core.jar" + #:source-dir "biojava-core/src/main/java/" + #:test-dir "biojava-core/src/test" + ;; These tests seem to require internet access. + #:test-exclude (list "**/SearchIOTest.java" + "**/BlastXMLParserTest.java" + "**/GenbankCookbookTest.java" + "**/GenbankProxySequenceReaderTest.java") + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-core/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-core/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Core libraries of Java framework for processing biological data") + (description "BioJava is a project dedicated to providing a Java framework +for processing biological data. It provides analytical and statistical +routines, parsers for common file formats, reference implementations of +popular algorithms, and allows the manipulation of sequences and 3D +structures. The goal of the biojava project is to facilitate rapid +application development for bioinformatics. + +This package provides the core libraries.") + (license license:lgpl2.1+))) -- 2.15.1