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gnu: Add java-biojava-core.
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
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@ -11949,3 +11949,59 @@ (define-public python-loompy
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graphs. This library makes it easy to work with @file{.loom} files for
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single-cell RNA-seq data.")
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(license license:bsd-3)))
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(define-public java-biojava-core
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(package
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(name "java-biojava-core")
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(version "4.2.11")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/biojava/biojava")
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(commit (string-append "biojava-" version))))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk"))))
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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-core.jar"
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#:source-dir "biojava-core/src/main/java/"
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#:test-dir "biojava-core/src/test"
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;; These tests seem to require internet access.
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#:test-exclude (list "**/SearchIOTest.java"
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"**/BlastXMLParserTest.java"
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"**/GenbankCookbookTest.java"
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"**/GenbankProxySequenceReaderTest.java")
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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-core/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-core/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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(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 "Core libraries of Java framework for processing biological data")
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(description "BioJava is a project dedicated to providing a Java framework
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for processing biological data. It provides analytical and statistical
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routines, parsers for common file formats, reference implementations of
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popular algorithms, and allows the manipulation of sequences and 3D
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structures. The goal of the biojava project is to facilitate rapid
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application development for bioinformatics.
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This package provides the core libraries.")
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(license license:lgpl2.1+)))
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