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gnu: Add java-biojava-alignment.

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* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
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Ricardo Wurmus 2018-03-01 19:41:42 +01:00 committed by Ricardo Wurmus
parent b28c803708
commit 22c09c335b
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gnu/packages/bioinformatics.scm
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@ -12212,3 +12212,47 @@ (define-public java-biojava-phylo
(synopsis "Biojava interface to the forester phylogenomics library") (synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the (description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees."))) forester phylogenomics library for constructing phylogenetic trees.")))
(define-public java-biojava-alignment
(package (inherit java-biojava-core)
(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)
("java-biojava-phylo" ,java-biojava-phylo)
("java-forester" ,java-forester)))
(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")))