From c8d71da303ff6b82a30db542d382cab57a00699e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 11 Dec 2014 17:37:16 +0100
Subject: [PATCH] gnu: Add bedtools

* gnu/packages/bioinformatics.scm (bedtools): New variable.
---
 gnu/packages/bioinformatics.scm | 68 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6f6178a..bcc5d43 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,74 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python))
 
+(define-public bedtools
+  (package
+    (name "bedtools")
+    (version "2.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+    (build-system gnu-build-system)
+    (inputs `(("python" ,python)
+              ("samtools" ,samtools)
+              ("zlib" ,zlib)))
+    (arguments
+     '(#:test-target "test"
+       #:phases
+       (alist-cons-after
+        'unpack 'patch-makefile-SHELL-definition
+                (lambda _
+                  ;; patch-makefile-SHELL cannot be used here as it does not
+                  ;; yet patch definitions with `:='.  Since changes to
+                  ;; patch-makefile-SHELL result in a full rebuild, features
+                  ;; of patch-makefile-SHELL are reimplemented here.
+                  (define (find-shell name)
+                    (let ((shell
+                           (search-path (search-path-as-string->list (getenv "PATH"))
+                                        name)))
+                      (unless shell
+                        (format (current-error-port)
+                                "patch-makefile-SHELL: warning: no binary for shell `~a' found in $PATH~%"
+                                name))
+                      shell))
+                  (substitute* "Makefile"
+                    (("^SHELL := .*$") (string-append "SHELL := " (find-shell "bash") " -e \n"))))
+                (alist-delete
+                 'configure
+                 (alist-replace
+                  'install (lambda* (#:key outputs #:allow-other-keys)
+                             (let* ((out (assoc-ref outputs "out"))
+                                    (bin (string-append out "/bin"))
+                                    (tools
+                                     '("bamToFastq" "mapBed" "shuffleBed" "bed12ToBed6" "bedToBam"
+                                       "multiIntersectBed" "complementBed" "randomBed" "tagBam" "sortBed"
+                                       "annotateBed" "clusterBed" "fastaFromBed" "coverageBed" "bedpeToBam"
+                                       "pairToPair" "subtractBed" "nucBed" "expandCols" "bedToIgv" "slopBed"
+                                       "closestBed" "windowMaker" "linksBed" "getOverlap" "mergeBed" "windowBed"
+                                       "flankBed" "pairToBed" "intersectBed" "bamToBed" "multiBamCov"
+                                       "unionBedGraphs" "genomeCoverageBed" "groupBy" "maskFastaFromBed"
+                                       "bedtools")))
+                               (mkdir-p bin)
+                               (map (lambda (tool)
+                                      (copy-file (string-append "bin/" tool)
+                                                 (string-append bin "/" tool)))
+                                    tools)))
+                  %standard-phases)))))
+    (home-page "https://github.com/arq5x/bedtools2")
+    (synopsis "Swiss army knife for genome arithmetic")
+    (description
+     "Collectively, the bedtools utilities are a swiss-army knife of tools for
+a wide-range of genomics analysis tasks.  The most widely-used tools enable
+genome arithmetic: that is, set theory on the genome.  For example, bedtools
+allows one to intersect, merge, count, complement, and shuffle genomic
+intervals from multiple files in widely-used genomic file formats such as BAM,
+BED, GFF/GTF, VCF.")
+    (license license:gpl2)))
+
 (define-public samtools
   (package
     (name "samtools")
-- 
1.9.3