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gnu: Add java-biojava-alignment-4.0.
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
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@ -12306,3 +12306,47 @@ (define-public java-biojava-phylo-4.0
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(synopsis "Biojava interface to the forester phylogenomics library")
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(description "The phylo module provides a biojava interface layer to the
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forester phylogenomics library for constructing phylogenetic trees.")))
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(define-public java-biojava-alignment-4.0
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(package (inherit java-biojava-core-4.0)
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(name "java-biojava-alignment")
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(build-system ant-build-system)
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(arguments
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`(#:jdk ,icedtea-8
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#:jar-name "biojava-alignment.jar"
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#:source-dir "biojava-alignment/src/main/java/"
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#:test-dir "biojava-alignment/src/test"
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#:phases
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(modify-phases %standard-phases
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(add-before 'build 'copy-resources
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(lambda _
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(copy-recursively "biojava-alignment/src/main/resources"
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"build/classes")
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#t))
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(add-before 'check 'copy-test-resources
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(lambda _
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(copy-recursively "biojava-alignment/src/test/resources"
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"build/test-classes")
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#t)))))
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(propagated-inputs
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`(("java-log4j-api" ,java-log4j-api)
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("java-log4j-core" ,java-log4j-core)
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("java-slf4j-api" ,java-slf4j-api)
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("java-slf4j-simple" ,java-slf4j-simple)
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("java-biojava-core" ,java-biojava-core-4.0)
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("java-biojava-phylo" ,java-biojava-phylo-4.0)
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("java-forester" ,java-forester-1.005)))
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(native-inputs
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`(("java-junit" ,java-junit)
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("java-hamcrest-core" ,java-hamcrest-core)))
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(home-page "http://biojava.org")
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(synopsis "Biojava API for genetic sequence alignment")
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(description "The alignment module of BioJava provides an API that
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contains
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@itemize
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@item implementations of dynamic programming algorithms for sequence
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alignment;
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@item reading and writing of popular alignment file formats;
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@item a single-, or multi- threaded multiple sequence alignment algorithm.
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@end itemize\n")))
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