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

Chris Fields cjfields at illinois.edu
Fri Oct 1 15:47:31 EDT 2010


Keiran,

We gladly accept patches if this is easier for you.  Using git/github is one way of getting more users involved and opening up the code more; the actual barrier to submit code changes is lowered to the point where one can fork our code and hack away, then submit pull requests for those changes to be merged (all via github, using one's account).  

We are generally doing more code review these days (asking for tests, requiring passing tests for inclusion, etc), but in this case that's probably not a problem.

chris

On Oct 1, 2010, at 10:45 AM, Scott Cain 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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> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
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