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:


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,

> 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
> mcdow...@vims.edu<mailto:mcdow...@vims.edu>
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