gnu: Add bowtie1.
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
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@ -1384,6 +1384,46 @@ gapped, local, and paired-end alignment modes.")
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(supported-systems '("x86_64-linux"))
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(license license:gpl3+)))
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(define-public bowtie1
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(package
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(name "bowtie1")
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(version "1.2.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
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version "/bowtie-" version "-src.zip"))
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(sha256
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(base32
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"1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0"))
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(modules '((guix build utils)))
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(snippet
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'(substitute* "Makefile"
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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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(arguments
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'(#:tests? #f ; no "check" target
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#:make-flags
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(list "all"
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(string-append "prefix=" (assoc-ref %outputs "out")))
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#:phases
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(modify-phases %standard-phases
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(delete 'configure))))
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(inputs
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`(("tbb" ,tbb)
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("zlib" ,zlib)))
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(supported-systems '("x86_64-linux"))
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(home-page "http://bowtie-bio.sourceforge.net/index.shtml")
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(synopsis "Fast aligner for short nucleotide sequence reads")
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(description
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"Bowtie is a fast, memory-efficient short read aligner. It aligns short
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DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
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reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to
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keep its memory footprint small: typically about 2.2 GB for the human
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genome (2.9 GB for paired-end).")
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(license license:artistic2.0)))
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(define-public tophat
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(package
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(name "tophat")
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