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09/17: gnu: Add java-biojava-phylo.


From: Ricardo Wurmus
Subject: 09/17: gnu: Add java-biojava-phylo.
Date: Sat, 3 Mar 2018 15:28:37 -0500 (EST)

rekado pushed a commit to branch master
in repository guix.

commit b28c803708d41c4a5323e31e01f7b6044fcc6dda
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Mar 1 19:41:41 2018 +0100

    gnu: Add java-biojava-phylo.
    
    * gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
---
 gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d64cda2..fbb3264 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12176,3 +12176,39 @@ application development for bioinformatics.
 
 This package provides the core libraries.")
     (license license:lgpl2.1+)))
+
+(define-public java-biojava-phylo
+  (package (inherit java-biojava-core)
+    (name "java-biojava-phylo")
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-phylo.jar"
+       #:source-dir "biojava-phylo/src/main/java/"
+       #:test-dir "biojava-phylo/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-phylo/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-phylo/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)
+       ("java-biojava-core" ,java-biojava-core)
+       ("java-forester" ,java-forester)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org";)
+    (synopsis "Biojava interface to the forester phylogenomics library")
+    (description "The phylo module provides a biojava interface layer to the
+forester phylogenomics library for constructing phylogenetic trees.")))



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