Jan; Thanks for getting back with all the detailed information. I dug into this further and understand what is happening: - tools/data_source/upload.py calls lib/galaxy/datatypes/sniff.py:stream_to_file - stream_to_file uses pythons tempfile module - tempfile defaults to using /tmp - As large files stream in the temporary space fills up, causing the issue you are seeing. The best way to work around this is to have the galaxy user on Amazon export TMPDIR to point at a temporary directory on /mnt/galaxyData instead of the root filesystem. I'm hoping that Enis or Dannon might be able to help out with the best place to set this in CloudMan to avoid the issue, I've cc'ed them in. If you want to manually fix it to get some work done, you could create a directory /mnt/galaxyData/tmp and then symlink /tmp there: ln -s /mnt/galaxyData/tmp /tmp Hope this helps and we can come up with a more permanent fix. Thanks again, Brad

Thanks Brad, Sorry it has taken me so long to respond. I had a meeting sort of day. I started another instance to recreate what is happening to me in more detail. I hope this helps. I tried to color code things so you could follow everything more easily.

This is what I have when I start up Galaxy through BioCloudCentral before I import any files...

Get cloud support with Ubuntu Advantage Cloud Guest http://www.ubuntu.com/business/services/cloud ubuntu@ip-10-44-78-218:~$ df -h Filesystem Size Used Avail Use% Mounted on /dev/xvda1 20G 13G 6.1G 68% / udev 8.4G 4.0K 8.4G 1% /dev tmpfs 3.4G 644K 3.4G 1% /run none 5.0M 0 5.0M 0% /run/lock none 8.4G 0 8.4G 0% /run/shm /dev/xvdb 404G 201M 383G 1% /mnt

After starting to import data (pasted https://s3.amazonaws.com/thunnus/BluefinAQ30_shuffled.fastq), it starts filling up immediately

Filesystem Size Used Avail Use% Mounted on /dev/xvda1 20G 19G 0 100% / udev 8.4G 4.0K 8.4G 1% /dev tmpfs 3.4G 660K 3.4G 1% /run none 5.0M 0 5.0M 0% /run/lock none 8.4G 0 8.4G 0% /run/shm /dev/xvdb 404G 201M 383G 1% /mnt /dev/xvdg1 700G 654G 47G 94% /mnt/galaxyIndices /dev/xvdg2 10G 1.7G 8.4G 17% /mnt/galaxyTools /dev/xvdg3 500G 81M 500G 1% /mnt/galaxyData