gnu: Add indelfixer.
* gnu/packages/bioinformatics.scm (indelfixer): New variable.
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@ -15570,6 +15570,41 @@ (define-public python-gffutils
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than is possible with plain-text methods alone.")
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(license license:expat))))
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(define-public indelfixer
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(package
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(name "indelfixer")
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(version "1.1")
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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/cbg-ethz/InDelFixer/")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"10ak05x8i1bx2p7rriv2rglqg1wr7c8wrhjrqlq1wm7ka99w8i79"))))
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(build-system ant-build-system)
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(arguments
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`(#:jar-name "InDelFixer.jar"
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#:source-dir "src/main/java"
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#:test-dir "src/test"))
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(inputs
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`(("java-commons-lang2" ,java-commons-lang)
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("java-args4j" ,java-args4j)))
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(native-inputs
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`(("java-junit" ,java-junit)))
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(home-page "https://github.com/cbg-ethz/InDelFixer/")
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(synopsis "Iterative and sensitive NGS sequence aligner")
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(description "InDelFixer is a sensitive aligner for 454, Illumina and
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PacBio data, employing a full Smith-Waterman alignment against a reference.
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This Java command line application aligns Next-Generation Sequencing (NGS) and
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third-generation reads to a set of reference sequences, by a prior fast k-mer
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matching and removes indels, causing frame shifts. In addition, only a
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specific region can be considered. An iterative refinement of the alignment
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can be performed, by alignment against the consensus sequence with wobbles.
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The output is in SAM format.")
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(license license:gpl3+)))
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(define-public libsbml
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(package
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(name "libsbml")
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