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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d3b891996d..2e786b3290 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -238,6 +238,53 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public bwa + (package + (name "bwa") + (version "0.7.12") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bio-bwa/bwa-" + version ".tar.bz2")) + (sha256 + (base32 + "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:phases + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append + (assoc-ref outputs "out") "/bin")) + (doc (string-append + (assoc-ref outputs "out") "/share/doc/bwa")) + (man (string-append + (assoc-ref outputs "out") "/share/man/man1"))) + (mkdir-p bin) + (mkdir-p doc) + (mkdir-p man) + (copy-file "bwa" (string-append bin "/bwa")) + (copy-file "README.md" (string-append doc "/README.md")) + (copy-file "bwa.1" (string-append man "/bwa.1")))) + ;; no "configure" script + (alist-delete 'configure %standard-phases)))) + (inputs `(("zlib" ,zlib))) + (home-page "http://bio-bwa.sourceforge.net/") + (synopsis "Burrows-Wheeler sequence aligner") + (description + "BWA is a software package for mapping low-divergent sequences against a +large reference genome, such as the human genome. It consists of three +algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is +designed for Illumina sequence reads up to 100bp, while the rest two for +longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar +features such as long-read support and split alignment, but BWA-MEM, which is +the latest, is generally recommended for high-quality queries as it is faster +and more accurate. BWA-MEM also has better performance than BWA-backtrack for +70-100bp Illumina reads.") + (license license:gpl3+))) + (define-public clipper (package (name "clipper") |