Question: Fail to reproduce galaxy job environment
1
gravatar for manuel.pasieka
8 months ago by
manuel.pasieka30 wrote:

Hi,

I have a Galaxy 16.10 instance submitting onto a PBS controlled cluster using the module system to resolve dependencies. Using the Picard CollectRnaSeqMetrics tool always fails because of the gtfToGenePred that it depends ons.

gtfToGenePred: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

The thing is that in order to debug errors like this, I normaly log onto the cluster using the same user as galaxy to submit jobs, then go into the job folder, and load the environment produced by the galaxy_XXX.sh and tool_script.sh files.

Hoping to get the have the same environment as the executing galaxy task.

Running the gtfToGenePred instructions manualy works out just fine, without any libpng issues.

How do you normaly debug such issues? Any ideas on what could be the problem?

thx! Manuel

job environment • 167 views
ADD COMMENTlink written 8 months ago by manuel.pasieka30
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