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: firstname.lastname@example.org [mailto:email@example.com] Namens Peter Cock Verzonden: maandag 13 februari 2012 11:04 Aan: Arthur Zheng CC: firstname.lastname@example.org Onderwerp: Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer
On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng email@example.com wrote:
On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock firstname.lastname@example.org wrote:
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng email@example.com wrote:
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:
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?
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:
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?
You must add library files to your current history via the "Shared Data" menu at the top of the Galaxy window.
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