Re: [galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

2016-03-19 Thread John Chilton
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 b

Re: [galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

2016-03-09 Thread Peter Briggs
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 l

[galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

2016-03-08 Thread Peter Briggs
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, bin