openms_msfraggeradapter error

[cat-bro]

ping @bernt-matthias

A Galaxy Australia user sent a report of MS Fragger Adapter failing with this stdout

Input file '/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar' could not be found (by searching on PATH). Either provide a full filepath or fix your PATH environment! Since this file is not strictly required, you might also pass the empty string "" as argument to prevent it's usage (this might limit the usability of the tool).
Error: File not found (the file '/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar' could not be found)

This looks like a bug but maybe it isn't - is this a path that would exist within a container?

[bernt-matthias]

Jep, bug. Its hardcoded here:

tools-galaxyp/tools/openms/MSFraggerAdapter.xml

Line 70 in 3ff8be1

<configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>

If one wants to use it the best idea would be yo change this to the tool directory and put the jar there.

Better solution is coming in here: bioconda/bioconda-recipes#45127