gnu: Add tetoolkit.
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.master
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@ -1752,6 +1752,72 @@ high-throughput sequencing data – with an emphasis on simplicity.")
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(define-public python2-plastid
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(define-public python2-plastid
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(package-with-python2 python-plastid))
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(package-with-python2 python-plastid))
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(define-public tetoolkit
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(package
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(name "tetoolkit")
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(version "2.0.3")
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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/mhammell-laboratory/tetoolkit.git")
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(commit 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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"1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2 ; not guaranteed to work with Python 3
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'make-writable
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(lambda _
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(for-each make-file-writable (find-files "."))
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#t))
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(add-after 'unpack 'patch-invocations
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* '("bin/TEtranscripts"
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"bin/TEcount")
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(("'sort ")
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(string-append "'" (which "sort") " "))
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(("'rm -f ")
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(string-append "'" (which "rm") " -f "))
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(("'Rscript'") (string-append "'" (which "Rscript") "'")))
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(substitute* "TEToolkit/IO/ReadInputs.py"
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(("BamToBED") (which "bamToBed")))
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(substitute* "TEToolkit/Normalization.py"
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(("\"Rscript\"")
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(string-append "\"" (which "Rscript") "\"")))
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#t))
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(add-after 'install 'wrap-program
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(lambda* (#:key outputs #:allow-other-keys)
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;; Make sure the executables find R packages.
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(let ((out (assoc-ref outputs "out")))
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(for-each
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(lambda (script)
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(wrap-program (string-append out "/bin/" script)
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`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
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'("TEtranscripts"
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"TEcount")))
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#t)))))
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(inputs
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`(("coreutils" ,coreutils)
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("bedtools" ,bedtools)
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("python-argparse" ,python2-argparse)
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("python-pysam" ,python2-pysam)
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("r-minimal" ,r-minimal)
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("r-deseq2" ,r-deseq2)))
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(home-page "https://github.com/mhammell-laboratory/tetoolkit")
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(synopsis "Transposable elements in differential enrichment analysis")
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(description
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"This is package for including transposable elements in differential
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enrichment analysis of sequencing datasets. TEtranscripts and TEcount take
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RNA-seq (and similar data) and annotates reads to both genes and transposable
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elements. TEtranscripts then performs differential analysis using DESeq2.
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Note that TEtranscripts and TEcount rely on specially curated GTF files, which
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are not included due to their size.")
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(license license:gpl3+)))
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(define-public cd-hit
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(define-public cd-hit
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(package
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(package
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(name "cd-hit")
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(name "cd-hit")
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