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gnu: Add repeat-masker.
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
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@ -2846,6 +2846,62 @@ (define-public trf
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bases are detected.")
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(license license:agpl3+)))
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(define-public repeat-masker
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(package
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(name "repeat-masker")
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(version "4.1.1")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://www.repeatmasker.org/"
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"RepeatMasker/RepeatMasker-"
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version ".tar.gz"))
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(sha256
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(base32 "03144sl9kh5ni2i33phi7x2pjndzbm5bjw3r4kqvmm6hxyb4k4x2"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #false ; there are none
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(replace 'build
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((share (string-append (assoc-ref outputs "out")
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"/share/RepeatMasker")))
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(mkdir-p share)
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(copy-recursively "." share)
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(with-directory-excursion share
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(invoke "perl" "configure"
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"--trf_prgm" (which "trf")
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"--hmmer_dir"
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(string-append (assoc-ref inputs "hmmer")
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"/bin"))))))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(share (string-append out "/share/RepeatMasker"))
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(bin (string-append out "/bin"))
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(path (getenv "PERL5LIB")))
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(install-file (string-append share "/RepeatMasker") bin)
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(wrap-program (string-append bin "/RepeatMasker")
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`("PERL5LIB" ":" prefix (,path ,share)))))))))
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(inputs
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`(("perl" ,perl)
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("perl-text-soundex" ,perl-text-soundex)
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("python" ,python)
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("python-h5py" ,python-h5py)
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("hmmer" ,hmmer)
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("trf" ,trf)))
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(home-page "https://github.com/Benson-Genomics-Lab/TRF")
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(synopsis "Tandem Repeats Finder: a program to analyze DNA sequences")
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(description "A tandem repeat in DNA is two or more adjacent, approximate
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copies of a pattern of nucleotides. Tandem Repeats Finder is a program to
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locate and display tandem repeats in DNA sequences. In order to use the
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program, the user submits a sequence in FASTA format. The output consists of
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two files: a repeat table file and an alignment file. Submitted sequences may
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be of arbitrary length. Repeats with pattern size in the range from 1 to 2000
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bases are detected.")
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(license license:osl2.1)))
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(define-public diamond
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(package
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(name "diamond")
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