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-rw-r--r--gn/packages/bioinformatics.scm46
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+)))