From 5fef15e50679a4e18df4fafede913c26d0029126 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:37 +0100
Subject: gnu: Add java-biojava-core.

* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
---
 gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 065dc477d8..4a90f30128 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11949,3 +11949,59 @@ (define-public python-loompy
 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+)))
-- 
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