There was some discussion of this on the bio-packaging list re changes in usage with Ricardo, but I think it breaks any dependent packages.
http://lists.open-bio.org/pipermail/bio-packaging/2015-July/000113.html
>From 3fd0b0c655c5f4f4317636f05d8242e2de9ae075 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
Date: Fri, 24 Jul 2015 23:11:31 +1000
Subject: [PATCH] gnu: bedtools: Update to 2.24.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..9cd661b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -148,7 +148,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/archive/v";
@@ -156,7 +156,7 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
-- 
2.4.3

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