diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37647a9b9b..f44dc32aa7 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 + +@itemize +@item implementations of dynamic programming algorithms for sequence + alignment; +@item reading and writing of popular alignment file formats; +@item a single-, or multi- threaded multiple sequence alignment algorithm. +@end itemize\n"))) |