Jan; No problem, sorry I don't have a nicer immediate solution for you. I appreciate the problem report and hopefully we'll figure out a clean fix for this. CloudBioLinux does have Velvet included by default, so you should be able to use it without needing to compile. Were you having trouble building, or running it? Velvet and other assemblers are memory hungry, so the issue you were seeing may be due to running out of memory. 'top' is a useful way to monitor memory usage from the console. If it is a memory issue, AWS does have some high-memory instances you could try: http://aws.amazon.com/ec2/instance-types/ I don't have a lot of experience doing assembly so unfortunately don't have good estimates for memory usage. It might be worth asking on the Velvet mailing list if you are still running into issues. Hope this helps, Brad

Thanks Brad,

I will see if I can do what you suggest-even if you are talking Klingon now:) . I really just want to use Velvet, so I may try to install it through CloudBioLinux-although last time I tried that I seemed to crash everything. I really need to get better at this stuff-or move to a place with bioinformatics support.

Many Many Thanks, Jan

On Mar 7, 2012, at 9:22 PM, Brad Chapman wrote:

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

Jan McDowell The Virginia Institute of Marine Science The College of William and Mary Department of Fisheries Science Phone: 804-684-7263 Fax: 804-684-7157 mcdowell@vims.edu<mailto:mcdowell@vims.edu>

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