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* [PATCH] Upgrade bedtools to 0.25.0.
@ 2016-01-09  6:47 Ben Woodcroft
  2016-01-09  9:54 ` Andreas Enge
  2016-01-09 18:07 ` Ricardo Wurmus
  0 siblings, 2 replies; 8+ messages in thread
From: Ben Woodcroft @ 2016-01-09  6:47 UTC (permalink / raw)
  To: guix-devel@gnu.org


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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


^ permalink raw reply related	[flat|nested] 8+ messages in thread

end of thread, other threads:[~2016-01-10 14:39 UTC | newest]

Thread overview: 8+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-01-09  6:47 [PATCH] Upgrade bedtools to 0.25.0 Ben Woodcroft
2016-01-09  9:54 ` 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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