> From: Fields, Christopher J [mailto:cjfie...@illinois.edu]
> [SNIP] if you follow the guidelines for FTP import, any method used
> (not just FTP, but scp, sftp, grid-ftp, etc.) to get data into the 'FTP' 
> import
> folder works as long as permissions on the data are set so the galaxy user on
> the cluster end can read the data.  

>From our investigations, the galaxy user needs to *own* the file, not just be 
>able to read it. The reason is that galaxy does a shutil.move, which calls 
>copy2 to give the new file the same permissions as the old, which calls 
>copystat, which calls os.chmod, which requires galaxy to be the owner.

This seems to be true at least on our old version of Galaxy, though perhaps 
it's been fixed in the last few months.

> We had our local cluster admins set up a
> link to the user's galaxy import folder in their home directory, so users can
> basically do this:
> 
>     scp mydata.fastq.gz usern...@biocluster.igb.illinois.edu:galaxy-upload

We wanted to do just that, but we kept getting permission errors. In the end, 
we needed to add a cron job that runs every minute as root and does a chown 
galaxy on any files appearing in the upload directories.

Please let me know if I'm missing something. I'd be happy to turn off the cron.

Thanks,

-Amir Karger



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