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 <command detect_errors="exit_code"></commands> this will more reasonably determine

if a tool failed based on the exit code.

To me this sounds like something that really should be fixed in the tool as presumably this affects every deployer.

Best,

Marius

On Mon, 27 Aug 2018 at 11:52, Matthias Bernt <m.bernt@ufz.de> wrote:

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

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt@ufz.de, www.ufz.de

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Prof. Dr. Dr. h.c. Georg Teutsch
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