From: Ricardo Wurmus <rekado@elephly.net>
To: 27175@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: bug#27175: [PATCH 1/6] gnu: Add ritornello.
Date: Wed, 31 May 2017 23:16:06 +0200 [thread overview]
Message-ID: <20170531211611.14094-1-rekado@elephly.net> (raw)
In-Reply-To: <87zids20kw.fsf@elephly.net>
* gnu/packages/bioinformatics.scm (ritornello): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ec69f5020..f2d92a888 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9185,3 +9185,48 @@ 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+)))
--
2.12.2
next prev parent reply other threads:[~2017-05-31 21:17 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-05-31 21:11 bug#27175: Some bioinfo tools Ricardo Wurmus
2017-05-31 21:16 ` Ricardo Wurmus [this message]
2017-05-31 21:16 ` bug#27175: [PATCH 2/6] gnu: Add trim-galore Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 3/6] gnu: Add gess Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 4/6] gnu: Add phylip Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 5/6] gnu: Add imp Ricardo Wurmus
2017-05-31 21:16 ` bug#27175: [PATCH 6/6] gnu: Add tadbit Ricardo Wurmus
2017-06-02 16:41 ` Leo Famulari
2017-06-09 1:33 ` Ricardo Wurmus
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