Hi Bjoern,
So, it seems that the best option is to:
- switching back to _JAVA_OPTIONS (which seems to be implemented also
on usegalaxy.org)
- handling the output in each java tool
This is also what usegalaxy.eu is using and we have special destinations
for java tools.
Indeed, this seems t
Hi Matthias,
Hi Marius,
Thanks for your comments. That's what I thought.
> To me this sounds like something that really should be fixed in the
> tool as presumably this affects every deployer.
Hmm. The 'tool' would be java. As far as I have seen java is
never/seldom in the tool dependencie
Hi Marius,
Thanks for your comments. That's what I thought.
> To me this sounds like something that really should be fixed in the
> tool as presumably this affects every deployer.
Hmm. The 'tool' would be java. As far as I have seen java is
never/seldom in the tool dependencies. Hence, the sys
Hi Matthias,
if a tool prints something to the stderr that is indeed considered to
indicate a failure, and it's the default mostly because
we don't want to break legacy tools that make this assumption. If you
include a profile version in your tool
or change your command section to this will more
Dear list,
I'm struggling to set java options for galaxy tools. Currently I use
` 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 wh
