@@ 9223,3 9223,48 @@ working with SAM and BAM files. Current parallelised functionality is
an important subset of samtools functionality, including view, index,
sort, markdup, and depth.")
(license license:gpl2+)))
+
+(define-public ritornello
+ (package
+ (name "ritornello")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/KlugerLab/"
+ "Ritornello/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-samtools-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("src/SamStream.h"
+ "src/BufferedGenomeReader.h")
+ (("<sam.h>") "<samtools/sam.h>"))
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/")))
+ (mkdir-p bin)
+ (install-file "bin/Ritornello" bin)
+ #t))))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("fftw" ,fftw)
+ ("boost" ,boost)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/KlugerLab/Ritornello")
+ (synopsis "Control-free peak caller for ChIP-seq data")
+ (description "Ritornello is a ChIP-seq peak calling algorithm based on
+signal processing that can accurately call binding events without the need to
+do a pair total DNA input or IgG control sample. It has been tested for use
+with narrow binding events such as transcription factor ChIP-seq.")
+ (license license:gpl3+)))