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
> 
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