[Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where should I submit a patch?

Dan Bolser dan.bolser at gmail.com
Tue Oct 5 06:07:36 EDT 2010


Here is a nice SVN to GIT conversion course:

http://git.or.cz/course/svn.html


On 1 October 2010 16:45, Scott Cain <scott at scottcain.net> wrote:
> Hi Keiran,
>
> Well, I've been told that it is easy for non-bioperl developers to use
> git to commit patches, and as if to prove it, there is a very long
> wiki page on the bioperl wiki describing how to use git:
>
>  http://www.bioperl.org/wiki/Using_Git
>
> I'm not sure what the right thing is to do; I'm cc'ing the bioperl
> list to get their input.
>
> Scott
>
>
> On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>> Hi all,
>>
>> Does anyone know how I should best get push a patch (new functionality) out
>> for this script which is part of the BioPerl package.
>>
>> I've added a 'fast' option which is useful for when you want to delete a
>> whole dataset.  The problem I was having is I loaded a large set of data
>> which had errors.  To delete it I tried to use the '-t' option but this
>> continually fails after several hours (eventually runs out of memory).  To
>> get round this I've added the '-f' flag which tells the script to perform
>> the delete/commit on each individual feature (and associated sub-features)
>> rather than attempt to do them all in a single commit.
>>
>> I've attached the modified version (unfortunately the formatting was kind of
>> knackered so a patch file will be a bit iffy).
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
>> charity registered in England with number 1021457 and acompany registered in
>> England with number 2742969, whose registeredoffice is 215 Euston Road,
>> London, NW1 2BE.
>>
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> kr2 at sanger.ac.uk
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>> and start using them to simplify application deployment and
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>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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