Galaxy devs,

I have just setup a Galaxy instance here in Cardiff University.  We have 
used a VM to host the web frontend and setup DRMAA to connect to our HPC 
resource.  We are still in the process of testing all the functionality it 
but one aspect which feels a bit strange is how to tell Galaxy to use the 
web frontend to run the tools which download data.  Our HPC resource does 
not have a connection to the outside world (only the login nodes).  I am 
not sure on the latest version but it seems handlers for tools can only be 
specified by id not by tool_type or any other "class" descriptor so 
non-computational tools can be run elsewhere whilst the computational 
tasks are run on HPC - I am currently using the id for each tool to 
specify a destination in the job_conf.xml.   Am I missing something 

Another aspect I found whilst installing this was the delicate nature of 
permissions when integrating it with the cluster.  This is especially true 
if ACLs are also used on the filesystem.  It seems the versions I 
installed (a version from November) could fail without much information 
why it failed in the logs.  Also had occasions where Galaxy never found 
out a job failed even though the log file had an error and traceback 
(usually when the DRMAA submit failed).  Any advice (or documentation) 
what the disk permissions should be?  And if anyone else is using NFS then 
root_squash on NFS really does cause issues.

So after a bit of tweaking and getting used to the structure of the code I 
got something which seemed to work - I have possible a few fixes which 
others might find useful mainly to give better feedback in the log.  Any 
advice how best to integrate these back to you - is there a ticketing 
system to track changes? I must really upgrade Galaxy to a more recent 
version to see whether these have already been fixed.

Many thanks for all the work that goes into Galaxy and look forward 
collaborating with the community.

All the best,


Thomas Green        Senior Programmer
ARCCA, Redwood Building (Tower), King Edward VII Avenue, Cardiff, Wales, 
CF10 3NB, UK
Tel: +44 (0)29 208 79269        Fax: +44 (0)29 208 70734
Email:        Web:

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