> 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/