gnu: Add StringTie.
* gnu/packages/bioinformatics.scm (stringtie): New variable.
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@ -3310,6 +3310,61 @@ features; exactSNP: a SNP caller that discovers SNPs by testing signals
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against local background noises.")
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against local background noises.")
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(license license:gpl3+)))
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(license license:gpl3+)))
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(define-public stringtie
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(package
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(name "stringtie")
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(version "1.2.1")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
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"stringtie-" version ".tar.gz"))
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(sha256
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(base32
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"1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(delete-file-recursively "samtools-0.1.18")
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#t))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no test suite
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#:phases
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(modify-phases %standard-phases
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;; no configure script
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(delete 'configure)
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(add-before 'build 'use-system-samtools
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(lambda _
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(substitute* "Makefile"
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(("stringtie: \\$\\{BAM\\}/libbam\\.a")
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"stringtie: "))
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(substitute* '("gclib/GBam.h"
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"gclib/GBam.cpp")
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(("#include \"(bam|sam|kstring).h\"" _ header)
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(string-append "#include <samtools/" header ".h>")))
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#t))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
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(install-file "stringtie" bin)
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#t))))))
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(inputs
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`(("samtools" ,samtools-0.1)
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("zlib" ,zlib)))
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(home-page "http://ccb.jhu.edu/software/stringtie/")
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(synopsis "Transcript assembly and quantification for RNA-Seq data")
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(description
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"StringTie is a fast and efficient assembler of RNA-Seq sequence
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alignments into potential transcripts. It uses a novel network flow algorithm
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as well as an optional de novo assembly step to assemble and quantitate
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full-length transcripts representing multiple splice variants for each gene
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locus. Its input can include not only the alignments of raw reads used by
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other transcript assemblers, but also alignments of longer sequences that have
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been assembled from those reads. To identify differentially expressed genes
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between experiments, StringTie's output can be processed either by the
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Cuffdiff or Ballgown programs.")
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(license license:artistic2.0)))
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(define-public vcftools
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(define-public vcftools
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(package
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(package
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(name "vcftools")
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(name "vcftools")
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