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