From: Ben Woodcroft <b.woodcroft@uq.edu.au>
To: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: [PATCH] Upgrade bedtools to 0.25.0.
Date: Sat, 9 Jan 2016 16:47:15 +1000 [thread overview]
Message-ID: <5690ACF3.7010206@uq.edu.au> (raw)
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A reasonably straightforward update.
Version 2.25.0 (3-Sept-2015)
1. Added new -F option that allows one to set the minimum fraction of
overlap required for the B interval. This complements the
functionality of the -f option.Available for intersect, coverage,
map, subtract, and jaccard.
2. Added new -e option that allows one to require that the minimum
fraction overlap is achieved in either A _OR_ B, not A _AND_ B which
is the behavior of the -r option. Available for intersect, coverage,
map, subtract, and jaccard.
3. Fixed a longstanding bug that prevented genomecov from reporting
chromosomes that lack a single interval.
4. Modified a src directory called "aux" to "driver" to prevent
compilation errors on Windows machines. Thanks very much to John
Marshall.
5. Fixed a regression that caused the coverage tool to complain if BED
files had less than 5 columns.
6. Fixed a variable overload bug that prevented compilation on Debian
machines.
7. Speedups to the groupby tool.
8. New -delim option for the groupby tool.
9. Fixed a bug in map that prevented strand-specifc overlaps from being
reported when using certain BEDPLUS formats.
10. Prevented excessive memory usage when not using pre-sorted input.
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From 0a1faccd5765b0005dccb4bdffb8badd87986286 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 9 Jan 2016 16:27:37 +1000
Subject: [PATCH] gnu: bedtools: Update to 2.25.0.
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition'
phase.
[source]: Remove patch merged upstream.
---
gnu/packages/bioinformatics.scm | 35 ++++++++++++-----------------------
1 file changed, 12 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c598327..55b7cb1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;;
@@ -207,7 +207,7 @@ computational cluster.")
(define-public bedtools
(package
(name "bedtools")
- (version "2.24.0")
+ (version "2.25.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
@@ -215,8 +215,7 @@ computational cluster.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
- (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
+ "1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m"))))
(build-system gnu-build-system)
(native-inputs `(("python" ,python-2)))
(inputs `(("samtools" ,samtools)
@@ -224,25 +223,15 @@ computational cluster.")
(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.
- (substitute* "Makefile"
- (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n"))))
- (alist-delete
- 'configure
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "bin" ".*"))))
- %standard-phases)))))
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*")))
+ #t)))))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Tools for genome analysis and arithmetic")
(description
--
2.6.3
next reply other threads:[~2016-01-09 6:47 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-01-09 6:47 Ben Woodcroft [this message]
2016-01-09 9:54 ` [PATCH] Upgrade bedtools to 0.25.0 Andreas Enge
2016-01-09 13:44 ` Pjotr Prins
2016-01-09 16:37 ` Andreas Enge
2016-01-09 17:48 ` Ludovic Courtès
2016-01-09 18:07 ` Ricardo Wurmus
2016-01-09 20:32 ` Leo Famulari
2016-01-10 14:39 ` Ben Woodcroft
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