Hey everybody,
I'm a newbie to galaxy and have been trying to wrap my head around the xml code needed to wrap tools in galaxy.
Below is the simple xml code I have been working with:
<tool id="biom_convert" name="Biom Convert">
<description>convert BIOM HDF5 format to BIOM JSON format</description>
<command interpreter="bash">biom convert -i $input -o $output --to-json</command>
<inputs>
<param format="biom" name="input" type="data" label="HDF5 input"/>
<param format="tabular" name="output" type="text" label="JSON output"/>
</inputs>
<outputs>
<data format="tabular" name="${output}" type="data" />
</outputs>
<help>
This tool converts BIOM HDF5 format files to BIOM JSON format files.
</help>
</tool>
When I run this command (after selecting the biom input and output files) the result file is empty (after successfully finishing job) and there is no error feedback. Anyone have ideas of what could be wrong or how I should troubleshoot?
Note that when I run the job on the command line it does work correctly. Also, the "biom" command is actually a bash script that runs this command:
exec pyqi --driver-name biom --command-config-module biom.interfaces.optparse.config -- "$@"
(pyqi is a python package... I still don't totally understand dependencies in galaxy, so I'm not sure whether this could be a problem or not)
Thanks in advance!
Gavin
when you run the job on the command line, do you run it as yourself or as the user your galaxy server is running as?
As the user the galaxy server is running as.