Yeah - your discoveries are exactly right. 16.04 has added the ability
to configure a bunch of extra things on a per-job-destination basis
but this isn't included yet - probably should be though. Pulsar would
be a way to go - hopefully soon Pulsar will be included with Galaxy
directly and it will be as easy as declaring a new job destination
(https://github.com/galaxyproject/galaxy/issues/1378) but I don't
think that will make it into 16.04.

-John

On Wed, Mar 9, 2016 at 2:41 PM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
> 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
>
> Peter
>
>
> On 08/03/16 09:37, Peter Briggs wrote:
>>
>> Hello
>>
>> 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 ->
>> .Call
>> 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
>> https://www.biostars.org/p/115452/).
>>
>> 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
>>
>
> --
> 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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