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| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-01-11 00:34:11 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-01-11 00:36:13 +1000 |
| commit | 9b9b7ffd8e1446574781bd02542bb171b0705248 (patch) | |
| tree | d233b1ae9df9df722a43b2f958fb62f62b8c6445 /gnu/packages/bioinformatics.scm | |
| parent | 6573ac82ad83cacd264ae20f9266d21cb5852f12 (diff) | |
| download | patches-9b9b7ffd8e1446574781bd02542bb171b0705248.tar patches-9b9b7ffd8e1446574781bd02542bb171b0705248.tar.gz | |
gnu: bedtools: Update to 2.25.0.
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'. Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 |
1 files changed, 3 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index df0e23da89..55b7cb1c86 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) @@ -225,16 +224,6 @@ computational cluster.") '(#:test-target "test" #:phases (modify-phases %standard-phases - (add-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"))) - #t)) (delete 'configure) (replace 'install (lambda* (#:key outputs #:allow-other-keys) |