From bca2c57658db1fdccca996cd59a3b43f739f0d87 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Mon, 26 Jun 2017 21:07:10 +1000
Subject: gnu: bamm: Use htslib-1.3.

* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
---
 gnu/packages/bioinformatics.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87da4aed15..53239cb697 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -248,7 +248,7 @@ structure of the predicted RNA.")
        ("python-nose" ,python2-nose)
        ("python-pysam" ,python2-pysam)))
     (inputs
-     `(("htslib" ,htslib)
+     `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
        ("samtools" ,samtools)
        ("bwa" ,bwa)
        ("grep" ,grep)
@@ -3079,6 +3079,20 @@ data.  It also provides the bgzip, htsfile, and tabix utilities.")
     ;; the rest is released under the Expat license
     (license (list license:expat license:bsd-3))))
 
+;; This package should be removed once no packages rely upon it.
+(define htslib-1.3
+  (package
+    (inherit htslib)
+    (version "1.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/samtools/htslib/releases/download/"
+                    version "/htslib-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
+
 (define-public idr
   (package
     (name "idr")
-- 
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