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| author | Ricardo Wurmus <rekado@elephly.net> | 2017-04-13 14:16:12 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-06-09 03:31:50 +0200 |
| commit | b8fffd3a53a6b588e3613272802db580994b9cb0 (patch) | |
| tree | e3f5f0a45dabd33332dbc4253c9cd0fb4fa1942b | |
| parent | 1dacc269567683cedc439545a8077e523a1ed94e (diff) | |
| download | patches-b8fffd3a53a6b588e3613272802db580994b9cb0.tar patches-b8fffd3a53a6b588e3613272802db580994b9cb0.tar.gz | |
gnu: Add ritornello.
* gnu/packages/bioinformatics.scm (ritornello): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bf4dd87eb3..d61f91fcad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+))) |