> I appreciate the help, I am in no way a competent UNIX/Linux user. I
> just have 2 shuffled fastq files in an S3 bucket-I pasted the URL for
> these into Galaxy's upload file URL/Text box and that seems to be
> where the trouble started. On my first try loading the data files, I
> got a message saying there was no disk space.

I'm trying to reproduce here but can't seem to figure out how the disk
is filling up. A new filesystem should look like:

$ df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/xvda1             20G   13G  6.1G  68% /
udev                  3.7G  4.0K  3.7G   1% /dev
tmpfs                 1.5G  660K  1.5G   1% /run
none                  5.0M     0  5.0M   0% /run/lock
none                  3.7G     0  3.7G   0% /run/shm
/dev/xvdb             414G  201M  393G   1% /mnt
/dev/xvdg1            700G  654G   47G  94% /mnt/galaxyIndices
/dev/xvdg2             10G  1.7G  8.4G  17% /mnt/galaxyTools
/dev/xvdg3            5.0G   81M  5.0G   2% /mnt/galaxyData

with 6Gb of free space on '/'. If you pasted a file, like:


into the text box, it should show up as:


in the /mnt/galaxyData mount, which has all of the space for storing
files. So I'm not sure exactly what is filling up your root
partition. Could you try checking a couple of places and see if any of
the filesystem usage is different from what we expect:

$ du -sh /home/ubuntu/
361M   /home/ubuntu/

$ sudo du -sh /var/log/
3.1M   /var/log/

I'm cc'ing Enis in case he has any other ideas where we might be
accidentally filling up the root filesystem.

Thanks again for the feedback and sorry about the problems,

> I tried again, and it
> worked.  Then, when I tried to run velveth, it got hung up again with
> the no disk space issue.  I browsed around in the /dev/xvda1 file
> system and there were quite a few files (I pasted them below).  I
> assumed they were files relating to BloudBioLinux and I was not sure
> if I could get rid of any of the files. It was nothing I put there.  I
> started the instance using BioCloudCentral.  Maybe it would be better
> to just start Galaxy the long way (choosing a public AMI under launch
> instance...)?
> ubuntu@ip-10-44-117-85:/$ ls
> bin   etc     initrd.img  lib64       mnt  proc  sbin     sys  var
> boot  export  lib         lost+found  opt  root  selinux  tmp  vmlinuz
> dev   home    lib32       media       pkg  run   srv      usr
> Thanks again,
> Jan
> On Mar 6, 2012, at 8:47 PM, Brad Chapman wrote:
> > 
> > Jan;
> > Glad to hear you got Galaxy running successfully. It sounds like
> > everything is good to go once we sort out the disk space issue.
> > 
> >>> However, when I try to use NX to get the virtual desktop going I get the
> >>> message usr/bin/nxserver: line 381: echo: write error: No space left
> >>> on device.
> >>> 
> >>> Using the df -h command, I get:
> >>> 
> >>> 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  202M  383G   1% /mnt
> >>> /dev/xvdg1            700G  654G   47G  94% /mnt/galaxyIndices
> >>> /dev/xvdg2             10G  1.7G  8.4G  17% /mnt/galaxyTools
> >>> /dev/xvdg3            200G   11G  190G   6% /mnt/galaxyData
> >>> 
> >>> 
> >>> So, I guess my question as a new user is: How do I point Galaxy and
> >>> CloudBioLinux to all of this unused space?
> > 
> > By default CloudMan will put files into /mnt/galaxyData. However, as
> > you noticed the main filesystem got filled up at some point. Could this
> > have happened while transferring files over from S3? Are there files in
> > your home directory that you could delete or move to /mnt/galaxyData to
> > free up space?
> > 
> > CloudBioLinux and CloudMan shouldn't put a large number of files in the
> > root directory, but when the root filesystem is full it's going to be
> > very unhappy. Once you manually clear up some room there hopefully
> > things will run smoother.
> > 
> > If that doesn't help let us know and we can dig into it further. Thanks,
> > Brad
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