Hi,

I've had a few email chats with the author of snpEff and the fly in the 
ointment from my perspective is getting the vcf files it needs through Galaxy. 
As I understand it there is no way currently of getting the BAM/SAM files into 
the right input format so snpEff can use it within a Galaxy setup. So, whatever 
you do you'll still need one or two command line steps. We have a copy of 
snpEff here at Bristol on our Galaxy and when we did that we then realised 
there was no Galaxy method (that we could think of) for getting the input file 
ready for snpEFF to use. This is a pity as its actually a very nice piece of 
software with a nice professional looking output.

Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






On 8 Nov 2011, at 13:55, Dannon Baker wrote:

> Hi Laura,
> 
> While the SNPeff developers have made Galaxy wrappers available, this is not 
> a tool we currently have installed for use on the Galaxy server at 
> main.g2.bx.psu.edu.  Off the top of my head, I don't know of any other public 
> Galaxy servers that offer this tool, but if you have access to a local or 
> cloud galaxy server you could use the provided wrapper to install the tool 
> for use there.
> 
> Thanks!
> 
> -Dannon
> 
> 
> 
> On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote:
> 
>> Hi,
>> 
>> I use the Galaxy server and was wondering how to use SNPeff tool? I have 
>> seen that it can be integrating with Galaxy on their website 
>> (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it 
>> on the server? Is it something that can be run on the server?
>> 
>> Best Wishes,
>> 
>> Laura
>> 
>> -- 
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>> 
>> 
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>  http://lists.bx.psu.edu/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

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