Re: Question on Illumina read data upload to Galaxy

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Re: Question on Illumina read data upload to Galaxy

Anton Nekrutenko
Jeff:

Unfortunately there is no straightforward way to do this in your  
context. Can you put the files somewhere else on the web and use URL  
upload?

anton


On Jun 2, 2010, at 12:05 PM, Whyte, Jeffrey wrote:

> Dear Dr. Nekrutenko,
>
> First of all, I would like to thank you and congratulate you and  
> your colleagues on providing such an excellent collaborative  
> resource with the Galaxy web application.  The interface and  
> tutorials are very professional, and the amount of time and effort  
> put into the project must have been immense.
>
> I had a question that I posted to the SeqAnswers Bioinformatics  
> Forum regarding upload of NGS files to the Galaxy server, but have  
> received no response.  I was hoping you could point me in the right  
> direction.
>
> I would like to upload Illumina FASTQ files to Galaxy via the FTP  
> URL method described on the Galaxy website.  However, our University  
> Bioinformatics facility states: "FTP connections from remote systems  
> are not allowed. Remote file transfer connections must be initiated  
> using a secure FTP (SFTP) client program that authenticates to the  
> server using SSH version 2".
>
> Is there any way that I can upload the file from our Linux system  
> (e.g. use FTP "PUT" to transfer the file to Galaxy)?  Uploading the  
> file directly from my desktop (OS X) takes hours, and I was hoping  
> that the FTP protocol would speed this process.
>
> Thank you in advance for any advice or assistance you can provide.
>
> Sincerely,
> Jeff Whyte
>
> -----
> Jeffrey J. Whyte, PhD
> Department of Biomedical Sciences
> University of Missouri-Columbia
>
>

Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



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