After a bit of detective work we found the reason for the discrepancy between @roselucia’s local result and those on usegalaxy.* instances: it’s caused by ambiguous dependency versioning.
I’ve documented the details and what we decided to do for usegalaxy.eu in https://github.com/usegalaxy-eu/usegalaxy-eu-tools/issues/249.
@jennaj note that with the change on the usegalaxy.eu side all tools from the vcflib tool collection could potentially give different results on usegalaxy.eu and usegalaxy.org at the seemingly same version - just as results may differ between local instances and usegalaxy.org.
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