diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2846f10eb..ff6c3379af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -77,6 +77,64 @@ intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.") (license license:gpl2))) +(define-public bowtie + (package + (name "bowtie") + (version "2.2.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn")) + (modules '((guix build utils))) + (snippet + '(substitute* "Makefile" + (("^CC = .*$") "CC = gcc") + (("^CPP = .*$") "CPP = g++") + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + (build-system gnu-build-system) + (inputs `(("perl" ,perl) + ("perl-clone" ,perl-clone) + ("perl-test-deep" ,perl-test-deep) + ("perl-test-simple" ,perl-test-simple) + ("python" ,python-2))) + (arguments + '(#:make-flags '("allall") + #:phases + (alist-delete + 'configure + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (for-each (lambda (file) + (copy-file file (string-append bin file))) + (find-files "." "bowtie2.*")))) + (alist-replace + 'check + (lambda* (#:key outputs #:allow-other-keys) + (system* "perl" + "scripts/test/simple_tests.pl" + "--bowtie2=./bowtie2" + "--bowtie2-build=./bowtie2-build")) + %standard-phases))))) + (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") + (synopsis "Fast and sensitive nucleotide sequence read aligner") + (description + "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing +reads to long reference sequences. It is particularly good at aligning reads +of about 50 up to 100s or 1,000s of characters, and particularly good at +aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the +genome with an FM Index to keep its memory footprint small: for the human +genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports +gapped, local, and paired-end alignment modes.") + (license license:gpl3+))) + (define-public samtools (package (name "samtools") |