From e62ffce538649f97da702fc1080fa06668df10e7 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 | 64 +++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 60cf6b7007..1f7972870c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5051,6 +5051,70 @@ (define-public r-zlibbioc
 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)
+                         (install-file file "./src/smithlab_cpp/"))
+                       (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"
+        ,(let ((commit "3723e2d"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/smithlabcode/smithlab_cpp.git")
+                   (commit commit)))
+             (file-name (string-append "smithlab_cpp-" commit "-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 genomic data produced by CLIP-seq and
+RIP-seq experiments.  It takes input in BED or BAM format and identifies
+regions of statistically significant read enrichment.  Additional covariates
+may optionally be provided to further inform the peak-calling process.")
+    (license license:gpl3+)))
+
 (define-public pepr
   (package
     (name "pepr")