Dear list,
I'm struggling to set java options for galaxy tools. Currently I use `<env file="job_setup_script.sh"/> in my job_conf.xml and in the script I explored two ways to set java options:
`_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"`
But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr which is be interpreted as error by some tools. If I'm correct this is currently the default .. I have seen this happening, but can't remember the name of the tool.
So I switched to this 'trick':
`alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'`
but the problem is that the tool script is called and not sourced and therefore aliases are not used (could this be changed?). Furthermore, for tools which explicitly set the java options my settings would be ignored anyway (an example is the MSGFPlusAdapter which calles `java -Xmx3500m` .. so my -Xmx is overwritten .. I passing GALAXY_MEMORY_MB to the corresponding parameter might be a solution for this tool).
Any thought or suggestions on how to set the parameters in a production environment are very welcome.
Cheers, Matthias