Are you sure the fastq's are in older format? Otherwise you won't need to groom 
the files anymore (as far as I understood) since the newer format is comparable 
Sanger quality score already.... Saves huge resources!
Alex

-----Oorspronkelijk bericht-----
Van: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] Namens Peter Cock
Verzonden: maandag 13 februari 2012 11:04
Aan: Arthur Zheng
CC: galaxy-user@lists.bx.psu.edu
Onderwerp: Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer

On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng <haoz...@gmail.com> wrote:
>
> On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>>
>> On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng <haoz...@gmail.com> wrote:
>> > Hi,
>> >
>> > I have downloaded and installed a local instance of galaxy on the 
>> > linux server using my user account according to here:
>> > http://main.g2.bx.psu.edu/
>> >
>> > Then I ran the following command:
>> >> sh run.sh
>> > and accessed galaxy through the local firefox browser on the server
>> > http://localhost:8080
>> >
>> > Now I am trying to use some NGS files for FASTQ Groomer. Each file 
>> > is in the server disk already, but very large (~8G each).
>> > I was not able to use the "upload file from your computer" function 
>> > under the "Get Data" tab (maybe because each file is too large).
>> >
>> > What am I supposed to do?
>> >
>> > Thank you!
>> >
>> > Arthur
>>
>> The method you tried "uploads" the file from your computer back to 
>> itself - making a copy as it goes with lots of overhead. You should 
>> probably consider the procedure here which allows you to avoid even 
>> making a copy on disk but point at the existing files already on the 
>> server:
>>
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%
>> 20Files
>>
>> Peter
>
> Hi Peter,
>
> I have followed the link you provided and selected the option "Upload 
> directory of files".
> Now my NGS data are in the library, and I am wondering how I can feed them to 
> FASTQ Groomer?
>
> Thanks!
>
>
> Arthur

You must add library files to your current history via the "Shared Data"
menu at the top of the Galaxy window.

Peter
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___________________________________________________________
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
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