13/17: gnu: Add java-biojava-alignment-4.0.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 9ac7db1830a1b324524aa7d383c5f1b5e348237f
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Mar 1 19:41:45 2018 +0100

    gnu: Add java-biojava-alignment-4.0.
    
    * gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New 
variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 37647a9..f44dc32 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12306,3 +12306,47 @@ contains
     (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.")))
+
+(define-public java-biojava-alignment-4.0
+  (package (inherit java-biojava-core-4.0)
+    (name "java-biojava-alignment")
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-alignment.jar"
+       #:source-dir "biojava-alignment/src/main/java/"
+       #:test-dir "biojava-alignment/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-alignment/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-alignment/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-4.0)
+       ("java-biojava-phylo" ,java-biojava-phylo-4.0)
+       ("java-forester" ,java-forester-1.005)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org";)
+    (synopsis "Biojava API for genetic sequence alignment")
+    (description "The alignment module of BioJava provides an API that
+contains
+
address@hidden
address@hidden implementations of dynamic programming algorithms for sequence
+  alignment;
address@hidden reading and writing of popular alignment file formats;
address@hidden a single-, or multi- threaded multiple sequence alignment 
algorithm.
address@hidden itemize\n")))