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05/11: gnu: bamm: Use htslib-1.3.
From: |
Ben Woodcroft |
Subject: |
05/11: gnu: bamm: Use htslib-1.3. |
Date: |
Sat, 22 Jul 2017 20:32:00 -0400 (EDT) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit bca2c57658db1fdccca996cd59a3b43f739f0d87
Author: Ben Woodcroft <address@hidden>
Date: Mon Jun 26 21:07:10 2017 +1000
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(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87da4ae..53239cb 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")
- branch master updated (c62d1a6 -> f3f68a4), Ben Woodcroft, 2017/07/22
- 03/11: gnu: samtools: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 06/11: gnu: python-pysam: Update to 0.11.2.2., Ben Woodcroft, 2017/07/22
- 01/11: gnu: samtools: Use "modify-phases" syntax., Ben Woodcroft, 2017/07/22
- 02/11: gnu: htslib: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 05/11: gnu: bamm: Use htslib-1.3.,
Ben Woodcroft <=
- 07/11: gnu: htslib: Update to 1.5., Ben Woodcroft, 2017/07/22
- 09/11: gnu: bcftools: Update to 1.5., Ben Woodcroft, 2017/07/22
- 04/11: gnu: bcftools: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 08/11: gnu: samtools: Update to 1.5., Ben Woodcroft, 2017/07/22
- 11/11: gnu: metabat: Update to 2.11.1., Ben Woodcroft, 2017/07/22
- 10/11: gnu: python-plastid: Update to 0.4.8., Ben Woodcroft, 2017/07/22