[PATCH] Upgrade bedtools to 0.25.0.

[PATCH] Upgrade bedtools to 0.25.0.

[Ben Woodcroft]

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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

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Andreas Enge]

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

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Pjotr Prins]

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.

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Andreas Enge]

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

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Ludovic Courtès]

Andreas Enge <andreas@enge.fr> skribis:

> 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.

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’.

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Ricardo Wurmus]

Ben Woodcroft <b.woodcroft@uq.edu.au> 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

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Leo Famulari]

On Sat, Jan 09, 2016 at 07:07:42PM +0100, Ricardo Wurmus wrote:
> 
> Ben Woodcroft <b.woodcroft@uq.edu.au> 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
> 
> 

Re: [PATCH] Upgrade bedtools to 0.25.0.

[Ben Woodcroft]

On 10/01/16 06:32, Leo Famulari wrote:
> On Sat, Jan 09, 2016 at 07:07:42PM +0100, Ricardo Wurmus wrote:
>> Ben Woodcroft <b.woodcroft@uq.edu.au> 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.
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