Just to follow up on my own questions, in case it's of interest to others:

-- Re specifying different job working directories on a per-tool basis:

Having spent a bit of time looking at the "advanced" sample job_conf.xml and also at the code for setting up and dispatching jobs, it looks to me like it is not possible to do this (i.e. specify different job working directories within different job destinations).

In fact as far as I can tell (I'm slightly lost within the Galaxy code at this point), it looks like the working directory is created within the job wrapper (via the objectstore interface) before the handler is assigned.

I'm wondering if a possible workaround might be to use Pulsar running on the same server, but it looks like a lot of overhead for my current problem (especially as I don't have any experience currently with using Pulsar).

-- Re cuffdiff cummeRbund SQLite database error:

It looks like changing the job_working_directory to a non-lustre filesystem fixes this problem.

Best wishes


On 08/03/16 09:37, Peter Briggs wrote:

I've encountered an issue with running the cuffdiff tool on our local
production Galaxy instance.

Specifically when a cummerbund SQLite database is requested as output
then the tool fails with an error:

Creating database ./cummeRbund.sqlite
Error in sqliteSendQuery(con, statement, bind.data) :
   error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) :
   error in statement: disk I/O error
Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery ->
Execution halted

Our Galaxy is configured to use a LustreFS scratch directory for the
'job_working_directory', which I understand is where each job will have
its own working directory created, and I'm wondering if the SQLite error
above is a manifestation of a general problem with SQLite on LustreFS
(see e.g. the answer to this BioStars question

The obvious workaround is to change 'job_working_directory', preferably
just for the cuffdiff tool. Does anyone know if it's possible to do this
i.e. set 'job_working_directory' on a per-tool basis?

(Also, has anyone else seen this specific problem with
cuffdiff/cummerbund/SQLite on their local Galaxy instances?)

Thanks for your help - any suggestions greatly appreciated,

Best wishes


Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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