On Nov 7, 2011, at 10:41 PM, Robert Day wrote:

No but worked round it by enabling the directory path load option in the .ini. This worked fine.

On a different note....if I want to install the missing tools eg bowtie should they just work if they are already on my computer and in my path? Do I have to point galaxy to them or their index files etc?

I have been using bowtie, samtools, fastqc etc from terminal.

Hi Rob, That they're on your $PATH is enough to execute them. Most can work with a reference genome in your history, but for larger ones (or those that you'd be using frequently) it's best to pre-build indexes and set up the paths to those indexes: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup --nate

Rob

Sent from my iPad

On 8/11/2011, at 9:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:

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On Oct 21, 2011, at 7:55 PM, Robert Day wrote:

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Hi, Sorry to bother you guys with such a simple thing. I'm quite new to the terminal and command line etc. so downloading and getting Galaxy running on my PC was a voyage of discovery! Anyhow, I have it, it's alive.......... just can't get any data in!

Have made myself an Admin User to create a data library, I point the importer at the files and it starts but never stops and remains at 0bytes. Have I forgotten to set something up?

Surely I can just dump all my files in a folder in the right place and go get it when I need it. Can't seem to find an idiots guide for setting this up for a local install (just me and my computer). Any pointers or helpful threads would be great.

Hi Rob,

Sorry for the delay in response. Were you ever able to successfully upload files to your local instance?

--nate

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Cheers Rob Sent from my PC ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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