gnu: Add bowtie
* gnu/packages/bioinformatics.scm (bowtie): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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@ -77,6 +77,64 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
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BED, GFF/GTF, VCF.")
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(license license:gpl2)))
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(define-public bowtie
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(package
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(name "bowtie")
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(version "2.2.4")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
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version ".tar.gz"))
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(sha256
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(base32
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"15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
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(modules '((guix build utils)))
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(snippet
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'(substitute* "Makefile"
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(("^CC = .*$") "CC = gcc")
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(("^CPP = .*$") "CPP = g++")
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;; replace BUILD_HOST and BUILD_TIME for deterministic build
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(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
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(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
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(build-system gnu-build-system)
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(inputs `(("perl" ,perl)
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("perl-clone" ,perl-clone)
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("perl-test-deep" ,perl-test-deep)
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("perl-test-simple" ,perl-test-simple)
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("python" ,python-2)))
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(arguments
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'(#:make-flags '("allall")
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#:phases
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(alist-delete
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'configure
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(alist-replace
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'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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(mkdir-p bin)
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(for-each (lambda (file)
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(copy-file file (string-append bin file)))
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(find-files "." "bowtie2.*"))))
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(alist-replace
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'check
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(lambda* (#:key outputs #:allow-other-keys)
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(system* "perl"
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"scripts/test/simple_tests.pl"
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"--bowtie2=./bowtie2"
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"--bowtie2-build=./bowtie2-build"))
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%standard-phases)))))
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(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
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(synopsis "Fast and sensitive nucleotide sequence read aligner")
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(description
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"Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
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reads to long reference sequences. It is particularly good at aligning reads
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of about 50 up to 100s or 1,000s of characters, and particularly good at
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aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
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genome with an FM Index to keep its memory footprint small: for the human
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genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
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gapped, local, and paired-end alignment modes.")
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(license license:gpl3+)))
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(define-public samtools
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(package
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(name "samtools")
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