Hi all,

Many thanks for that Peter. It worked a charm. 

There does seem to be a bug in there somewhere. If more than one item is 
selected for retrieval at a time, only a single item is returned. The other 
items all return a 'This file cannot be found' error. 

Finally as an aside, could this system be adapted to retrieve the PTT files 
from Genbank?

All the very best,

Konrad.

-----Original Message-----
From: p.j.a.c...@googlemail.com [mailto:p.j.a.c...@googlemail.com] On Behalf Of 
Peter
Sent: 06 January 2011 15:55
To: Paszkiewicz, Konrad
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Easy download/setup of Bacterial Genbank and multiple 
alignment files from UCSC?

On Thu, Jan 6, 2011 at 3:24 PM, Paszkiewicz, Konrad
<k.h.paszkiew...@exeter.ac.uk> wrote:
> Happy new year to you!
>
> First of all, well done on a fabulous system. It really is going to make my
> life as a bioinformatician a lot easier and hopefully empower my wet-lab
> biologists.
>
> I'm trying to setup the 'Get microbial data' tool. Is there an easy way to
> get hold of these datasets easily with the location files and tool
> configuration files preset. I wouldn't like to have to try to setup
> thousands of genomes manually. Better still, can I set up my galaxy instance
> to send the request to your server directly?
>
> Thanks!
>
> Konrad.

See this thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004074.html

The summary is that the current code needs some updating to work
with the current NCBI FTP site (see my branch for some fixes), and
Dan will hopefully be looking at updating things - possibly to take
advantage of the Galaxy Library functionality (so that using the data
doesn't needless make a copy of it).

Peter

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