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 <n...@bx.psu.edu> wrote:
>
>> On Oct 21, 2011, at 7:55 PM, Robert Day wrote:
>>
>>> 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
>>
>>>
>>> Cheers Rob
>>> Sent from my PC
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>
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