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[bug#30666] [PATCH 05/17] gnu: Add java-biojava-core.
From: |
Ricardo Wurmus |
Subject: |
[bug#30666] [PATCH 05/17] gnu: Add java-biojava-core. |
Date: |
Thu, 1 Mar 2018 19:41:37 +0100 |
* 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
- [bug#30666] [PATCH 00/17] Add dropseq-tools., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 01/17] gnu: Add java-la4j., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 04/17] gnu: Add java-jdistlib., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 05/17] gnu: Add java-biojava-core.,
Ricardo Wurmus <=
- [bug#30666] [PATCH 06/17] gnu: Add java-openchart2., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 07/17] gnu: Add java-forester., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 10/17] gnu: Add java-biojava-alignment., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 08/17] gnu: Add java-forester-1.005., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 11/17] gnu: Add java-biojava-core-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 03/17] gnu: Add java-jtransforms., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 09/17] gnu: Add java-biojava-phylo., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 02/17] gnu: Add java-jlargearrays., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 12/17] gnu: Add java-biojava-phylo-4.0., Ricardo Wurmus, 2018/03/01
- [bug#30666] [PATCH 13/17] gnu: Add java-biojava-alignment-4.0., Ricardo Wurmus, 2018/03/01