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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-03-06 15:25:37 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-03-06 15:32:45 +0100 |
| commit | afeb10a056e1f5f2c492ace9ee0a33f09cb53e8a (patch) | |
| tree | f1554c0b6bd24ae40c21b235bfa4171d0dd3a8cb /gnu | |
| parent | 5b8f892872a3d0514d099c20bfa49035906e6320 (diff) | |
| download | patches-afeb10a056e1f5f2c492ace9ee0a33f09cb53e8a.tar patches-afeb10a056e1f5f2c492ace9ee0a33f09cb53e8a.tar.gz | |
gnu: Add bowtie1.
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 092c49d8cb..4b775d8b7d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1384,6 +1384,46 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public bowtie1 + (package + (name "bowtie1") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" + version "/bowtie-" version "-src.zip")) + (sha256 + (base32 + "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0")) + (modules '((guix build utils))) + (snippet + '(substitute* "Makefile" + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; no "check" target + #:make-flags + (list "all" + (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("tbb" ,tbb) + ("zlib" ,zlib))) + (supported-systems '("x86_64-linux")) + (home-page "http://bowtie-bio.sourceforge.net/index.shtml") + (synopsis "Fast aligner for short nucleotide sequence reads") + (description + "Bowtie is a fast, memory-efficient short read aligner. It aligns short +DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp +reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to +keep its memory footprint small: typically about 2.2 GB for the human +genome (2.9 GB for paired-end).") + (license license:artistic2.0))) + (define-public tophat (package (name "tophat") |