FTP Upload to Galaxy

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Here is the help: https://galaxyproject.org/support/loading-data/

Best, Jen, Galaxy team

ADD COMMENT • link modified 10 months ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jennifer that was very helpful, I will CyberDuck. Do you know if the file has to be uncompressed first or not? Do I have to specify the path, if not where does the data go? LeeAnn

ADD REPLY • link written 3.1 years ago by rooneyl • 0

Filezilla is a better choice now, but really you can use whatever FTP client you want, as long as passive FTP is present (or not use a client and just connect on the command-line).

The data goes into a holding area specific to your account. Any files you load will be available under the Upload tool where they can be moved into a history for use with tools.

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer, Thanks, that was helpful and I did get my files ftp'ed to Galaxy. I am processing as usual, which involves five simple steps.

1) upload reads 2) convert format from FASTQ to FASTA 3) Clip Adaptor sequence and all sequence 3' of the adaptor on reads 4) upload fasta reference sequence (human CFTR) 5) Align reads to reference sequence using LASTZ (very high stringency, see second screen shot)

So again the LASTZ is hung (gray) waiting to run, see first screen shot. Do you have anyway of moving my jobs up in the queue or checking to be sure that these are indeed going to eventually run? I have 6 total.

Thanks, LeeAnn

P.S. we are also setting up a cloud based Galaxy at OHSU in hopes of expediting this data analysis, but customizing it may take some time...

ADD REPLY • link written 3.1 years ago by rooneyl • 0

A grey dataset is queued. This occurs when either you have other jobs queued/running that were started before this one, or the Galaxy cluster is simply busy. Give it time as allowing it to execute is the best. If you delete and restart, the job just goes back to the end of the queue.

https://galaxyproject.org/support/how-jobs-execute/

Jen

ADD REPLY • link modified 10 months ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »