Glen:

Please, contribute it to Tool Shed once you are done with testing. This will be 
much appreciated.

Thanks!

anton


Anton Nekrutenko
http://galaxyproject.org




On Oct 12, 2011, at 4:00 PM, Glen Beane wrote:

> I have an mpileup tool for Galaxy I've developed.  After a little more 
> testing I may be able to share it.
> 
> the tool also converts the bcl output of mpileup to vcf
> 
> 
> On Oct 12, 2011, at 2:41 PM, Jennifer Jackson wrote:
> 
>> Hello David,
>> 
>> An update is planned, but we can't provide an exact time-line yet. To track 
>> the issue, this bitbucket ticket can be followed:
>> https://bitbucket.org/galaxy/galaxy-central/issue/524/
>> 
>> Apologies for the delay in reply,
>> 
>> Best,
>> 
>> Jen
>> Galaxy team
>> 
>> On 8/23/11 9:10 AM, David Hoover wrote:
>>> Is there any good reason why Galaxy can't use a more recent version of 
>>> samtools?  The only difference I can see is the mpileup command.  The 
>>> algorithm by which mpileup finds SNPs is a little different.  Does anyone 
>>> know if the file format has changed?  The only files that need to change 
>>> are sam_pileup.py and sam_pileup.xml.
>>> 
>>> David Hoover
>>> Helix Systems Staff
>>> http://helix.nih.gov
>>> ___________________________________________________________
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>> 
>> -- 
>> Jennifer Jackson
>> http://usegalaxy.org
>> http://galaxyproject.org/Support
>> ___________________________________________________________
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> 
> --
> Glen L. Beane
> Senior Software Engineer
> The Jackson Laboratory
> (207) 288-6153
> 
> 
> ___________________________________________________________
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