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| -rw-r--r-- | gn/packages/bioinformatics.scm | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 49e54ee..5bf7843 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -814,3 +814,49 @@ format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) +(define-public pindel + (package + (name "pindel") + (version "0.2.5b8") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/genome/pindel/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "06bsf0psxwf7h5p3j97xkh9k5qrwhxh6xn942y1j1m2inyhgs8bz")))) + (build-system gnu-build-system) + (inputs + `(("samtools" ,samtools) + ("htslib" ,htslib) + ("zlib" ,zlib))) + (native-inputs + `(("cppcheck" ,cppcheck) + ("python" ,python-2) + ("perl" ,perl))) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + ;; The first run creates a Makefile.local file. + (system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools"))) + ;; The second run actually compiles the program. + (zero? (system* "make")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "src/pindel" bin) + (install-file "src/pindel2vcf" bin) + (install-file "src/pindel2vcf4tcga" bin) + (install-file "src/sam2pindel" bin))))))) + (home-page "https://github.com/genome/pindel") + (synopsis "Structural variants detector for next-gen sequencing data") + (description "Pindel can detect breakpoints of large deletions, medium sized +insertions, inversions, tandem duplications and other structural variants at +single-based resolution from next-gen sequence data. It uses a pattern growth +approach to identify the breakpoints of these variants from paired-end short +reads.") + (license license:gpl3+))) |