From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: [PATCH] Add Piranha.
Date: Tue, 26 Apr 2016 16:09:41 +0200 [thread overview]
Message-ID: <idj8u008nru.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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From 8ebcd50666e13407d2b74907c9bc5e37ee420192 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 26 Apr 2016 16:08:47 +0200
Subject: [PATCH] gnu: Add Piranha.
* gnu/packages/bioinformatics.scm (piranha): New variable.
---
gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 62 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35c3334..7a93c72 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5209,6 +5209,68 @@ two-dimensional genome scans.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public piranha
+ (package
+ (name "piranha")
+ (version "1.1.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/smithlabcode/piranha"
+ "/archive/svn/tags/piranha-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'copy-smithlab-cpp
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir "src/smithlab_cpp")
+ (for-each (lambda (file)
+ (copy-file file
+ (string-append "./src/smithlab_cpp/"
+ (basename file))))
+ (find-files (assoc-ref inputs "smithlab-cpp")))
+ #t))
+ (add-after 'install 'install-to-store
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*")))
+ #t)))
+ #:configure-flags
+ (list (string-append "--with-bam_tools_headers="
+ (assoc-ref %build-inputs "bamtools") "/include/bamtools")
+ (string-append "--with-bam_tools_library="
+ (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
+ (inputs
+ `(("bamtools" ,bamtools)
+ ("samtools" ,samtools-0.1)
+ ("gsl" ,gsl)
+ ("smithlab-cpp"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (commit "3723e2d")))
+ (file-name "smithlab_cpp-3723e2d-checkout")
+ (sha256
+ (base32
+ "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (home-page "https://github.com/smithlabcode/piranha")
+ (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
+ (description
+ "Piranha is a peak-caller for CLIP-seq and RIP-seq data.")
+ (license license:gpl3+)))
+
(define-public pepr
(package
(name "pepr")
--
2.7.3
next reply other threads:[~2016-04-26 14:10 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-04-26 14:09 Ricardo Wurmus [this message]
2016-04-27 12:30 ` [PATCH] Add Piranha Ludovic Courtès
2016-05-19 9:27 ` Ricardo Wurmus
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