From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 9 Jan 2016 16:47:15 +1000 Message-ID: <5690ACF3.7010206@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------030809010606050602040908" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46399) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHnJ8-0005YX-UO for guix-devel@gnu.org; Sat, 09 Jan 2016 01:47:28 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aHnJ5-0002Hp-JX for guix-devel@gnu.org; Sat, 09 Jan 2016 01:47:26 -0500 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:41225 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHnJ5-0002HG-0I for guix-devel@gnu.org; Sat, 09 Jan 2016 01:47:23 -0500 Received: from smtp2.soe.uq.edu.au (smtp2.soe.uq.edu.au [10.138.113.41]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id u096lHtK031232 for ; Sat, 9 Jan 2016 16:47:18 +1000 Received: from [192.168.1.105] (static.customers.nuskope.com.au [103.25.181.216] (may be forged)) (authenticated bits=0) by smtp2.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id u096lFgp059300 (version=TLSv1.2 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Sat, 9 Jan 2016 16:47:17 +1000 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------030809010606050602040908 Content-Type: multipart/alternative; boundary="------------030309080707000206030605" --------------030309080707000206030605 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit 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. --------------030309080707000206030605 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit 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.
--------------030309080707000206030605-- --------------030809010606050602040908 Content-Type: text/x-patch; name="0001-gnu-bedtools-Update-to-2.25.0.patch" Content-Disposition: attachment; filename="0001-gnu-bedtools-Update-to-2.25.0.patch" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id u096lHtK031232 >From 0a1faccd5765b0005dccb4bdffb8badd87986286 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft 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-definitio= n' 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/bioinformatic= s.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 =C2=A9 2014, 2015 Ricardo Wurmus -;;; Copyright =C2=A9 2015 Ben Woodcroft +;;; Copyright =C2=A9 2015, 2016 Ben Woodcroft ;;; Copyright =C2=A9 2015 Pjotr Prins ;;; Copyright =C2=A9 2015 Andreas Enge ;;; @@ -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/ar= chive/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.p= atch"))))) + "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 `:=3D'. Since changes to - ;; patch-makefile-SHELL result in a full rebuild, features - ;; of patch-makefile-SHELL are reimplemented here. - (substitute* "Makefile" - (("^SHELL :=3D .*$") (string-append "SHELL :=3D " (which "ba= sh") " -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 --=20 2.6.3 --------------030809010606050602040908--