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-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: Andreas Enge Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 9 Jan 2016 10:54:42 +0100 Message-ID: <20160109095442.GB4285@debian> References: <5690ACF3.7010206@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41419) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHqEd-0007qF-9T for guix-devel@gnu.org; Sat, 09 Jan 2016 04:54:59 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aHqEa-0001j0-5N for guix-devel@gnu.org; Sat, 09 Jan 2016 04:54:59 -0500 Received: from mout.kundenserver.de ([217.72.192.74]:54351) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHqEZ-0001iw-SK for guix-devel@gnu.org; Sat, 09 Jan 2016 04:54:56 -0500 Content-Disposition: inline In-Reply-To: <5690ACF3.7010206@uq.edu.au> 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: Ben Woodcroft Cc: "guix-devel@gnu.org" On Sat, Jan 09, 2016 at 04:47:15PM +1000, Ben Woodcroft wrote: > A reasonably straightforward update. If I remember correctly, it is common practice to do the move to modify-phases and the update in two separate commits. Andreas From mboxrd@z Thu Jan 1 00:00:00 1970 From: Pjotr Prins Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 9 Jan 2016 14:44:19 +0100 Message-ID: <20160109134419.GA19838@thebird.nl> References: <5690ACF3.7010206@uq.edu.au> <20160109095442.GB4285@debian> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45336) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHtoz-00067K-GG for guix-devel@gnu.org; Sat, 09 Jan 2016 08:44:46 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aHtow-0003j4-Ai for guix-devel@gnu.org; Sat, 09 Jan 2016 08:44:45 -0500 Received: from mail.thebird.nl ([95.154.246.10]:40452) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHtow-0003ip-59 for guix-devel@gnu.org; Sat, 09 Jan 2016 08:44:42 -0500 Content-Disposition: inline In-Reply-To: <20160109095442.GB4285@debian> 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: Andreas Enge Cc: "guix-devel@gnu.org" On Sat, Jan 09, 2016 at 10:54:42AM +0100, Andreas Enge wrote: > On Sat, Jan 09, 2016 at 04:47:15PM +1000, Ben Woodcroft wrote: > > A reasonably straightforward update. > > If I remember correctly, it is common practice to do the move to modify-phases > and the update in two separate commits. Sometimes I wonder if we are not being too prissy. Not exactly taxing to read it in one commit and we can trust the committer to test it. I see the point of agreed layouts and putting things in a *single* commit. Now, for a change, we need two. Pj. From mboxrd@z Thu Jan 1 00:00:00 1970 From: Andreas Enge Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 9 Jan 2016 17:37:15 +0100 Message-ID: <20160109163715.GA12060@debian> References: <5690ACF3.7010206@uq.edu.au> <20160109095442.GB4285@debian> <20160109134419.GA19838@thebird.nl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37007) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHwWJ-0007J6-Fr for guix-devel@gnu.org; Sat, 09 Jan 2016 11:37:40 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aHwWG-0000U2-AZ for guix-devel@gnu.org; Sat, 09 Jan 2016 11:37:39 -0500 Received: from mout.kundenserver.de ([212.227.126.134]:54250) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHwWG-0000To-1U for guix-devel@gnu.org; Sat, 09 Jan 2016 11:37:36 -0500 Content-Disposition: inline In-Reply-To: <20160109134419.GA19838@thebird.nl> 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: Pjotr Prins Cc: "guix-devel@gnu.org" On Sat, Jan 09, 2016 at 02:44:19PM +0100, Pjotr Prins wrote: > Sometimes I wonder if we are not being too prissy. Not exactly taxing > to read it in one commit and we can trust the committer to test it. I > see the point of agreed layouts and putting things in a *single* > commit. Now, for a change, we need two. I do not have very strong feelings about the matter, but I do see the point of separating stylistic and syntactic changes on one hand from functional changes on the other hand. Then one can simply accept the former without further checking; and the latter does not require any checking since only the version and the hash line have changed. Probably it would then be okay to push these two commits directly without posting the patches to the list first. Andreas From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 09 Jan 2016 18:48:03 +0100 Message-ID: <87d1tabq5o.fsf@gnu.org> References: <5690ACF3.7010206@uq.edu.au> <20160109095442.GB4285@debian> <20160109134419.GA19838@thebird.nl> <20160109163715.GA12060@debian> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55623) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHxcZ-0002st-Af for guix-devel@gnu.org; Sat, 09 Jan 2016 12:48:12 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aHxcU-0002Cg-D9 for guix-devel@gnu.org; Sat, 09 Jan 2016 12:48:11 -0500 In-Reply-To: <20160109163715.GA12060@debian> (Andreas Enge's message of "Sat, 9 Jan 2016 17:37:15 +0100") 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: Andreas Enge Cc: "guix-devel@gnu.org" Andreas Enge skribis: > I do not have very strong feelings about the matter, but I do see the poi= nt > of separating stylistic and syntactic changes on one hand from functional > changes on the other hand. Then one can simply accept the former without > further checking; and the latter does not require any checking since only > the version and the hash line have changed. Right. Another practical advantage is that, should the upgrade cause problems, we can simply revert the commit that does the upgrade without losing the other change. Ludo=E2=80=99. From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 09 Jan 2016 19:07:42 +0100 Message-ID: <87io324oep.fsf@elephly.net> References: <5690ACF3.7010206@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60125) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHxvg-0005fw-NG for guix-devel@gnu.org; Sat, 09 Jan 2016 13:07:57 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aHxvc-0007Ah-NJ for guix-devel@gnu.org; Sat, 09 Jan 2016 13:07:56 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:25633) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aHxvc-0007AS-Df for guix-devel@gnu.org; Sat, 09 Jan 2016 13:07:52 -0500 In-reply-to: <5690ACF3.7010206@uq.edu.au> 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: Ben Woodcroft Cc: "guix-devel@gnu.org" Ben Woodcroft writes: > A reasonably straightforward update. I think you forgot to also remove the “bedtools-32bit-compilation.patch” file from “gnu/packages/patches”. Otherwise I agree with Andreas about separating the stylistic from the functional changes by doing two commits. Thanks! ~~ Ricardo From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Sat, 9 Jan 2016 15:32:10 -0500 Message-ID: <20160109203210.GC30687@jasmine> References: <5690ACF3.7010206@uq.edu.au> <87io324oep.fsf@elephly.net> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43092) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aI0BF-00036p-0h for guix-devel@gnu.org; Sat, 09 Jan 2016 15:32:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aI0BB-0004kN-Ro for guix-devel@gnu.org; Sat, 09 Jan 2016 15:32:08 -0500 Received: from out4-smtp.messagingengine.com ([66.111.4.28]:54210) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aI0BB-0004kD-Oy for guix-devel@gnu.org; Sat, 09 Jan 2016 15:32:05 -0500 Content-Disposition: inline In-Reply-To: <87io324oep.fsf@elephly.net> 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: Ricardo Wurmus Cc: "guix-devel@gnu.org" On Sat, Jan 09, 2016 at 07:07:42PM +0100, Ricardo Wurmus wrote: > > Ben Woodcroft writes: > > > A reasonably straightforward update. > > I think you forgot to also remove the “bedtools-32bit-compilation.patch” > file from “gnu/packages/patches”. In that case, the patch can also be "de-listed" from gnu-system.am, unless it is being used by another package. > > Otherwise I agree with Andreas about separating the stylistic from the > functional changes by doing two commits. > > Thanks! > > ~~ Ricardo > > From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Upgrade bedtools to 0.25.0. Date: Mon, 11 Jan 2016 00:39:18 +1000 Message-ID: <56926D16.5020001@uq.edu.au> References: <5690ACF3.7010206@uq.edu.au> <87io324oep.fsf@elephly.net> <20160109203210.GC30687@jasmine> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38613) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aIH9e-00075g-LY for guix-devel@gnu.org; Sun, 10 Jan 2016 09:39:39 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aIH9b-000426-Gn for guix-devel@gnu.org; Sun, 10 Jan 2016 09:39:38 -0500 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:37258 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aIH9a-00041M-UA for guix-devel@gnu.org; Sun, 10 Jan 2016 09:39:35 -0500 In-Reply-To: <20160109203210.GC30687@jasmine> 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: Leo Famulari , Ricardo Wurmus Cc: "guix-devel@gnu.org" On 10/01/16 06:32, Leo Famulari wrote: > On Sat, Jan 09, 2016 at 07:07:42PM +0100, Ricardo Wurmus wrote: >> Ben Woodcroft writes: >> >>> A reasonably straightforward update. >> I think you forgot to also remove the =E2=80=9Cbedtools-32bit-compilat= ion.patch=E2=80=9D >> file from =E2=80=9Cgnu/packages/patches=E2=80=9D. > In that case, the patch can also be "de-listed" from gnu-system.am, > unless it is being used by another package. Oh yes, those. > >> Otherwise I agree with Andreas about separating the stylistic from the >> functional changes by doing two commits. Pushed as two commits, thanks. ben