We have configured galaxy to work with our SGE cluster using drmaa job runner interface. We are using 'unified method' for this install and both TEMP environment variable and new_file_path in universe_wsgi.ini file have been configured correctly. However, we are seeing some errors where local /tmp space on compute nodes is being referenced by the galaxy tools. Specifically we saw it mentioned in error messages from following tools: * bwa_wrapper and upload tools: 'No space left on device: /tmp...' * sam_to_bam tool: 'Error sorting alignments from /tmp/filename..'
Shouldn't it be referencing TEMP environment variable or new_file_path configuration value? Is it getting overridden by TMP or TMPDIR variables in python wrapper code? Has anyone else experienced similar issue?
-- Thanks, Shantanu.