5 days ago by
Picard installs correctly in a default 17_05 (http://usegalaxy.org) without any dependency config changes if Conda is already on your computer/server. I tested with this version of Picard.
Update your Galaxy instance if needed and use the latest Picard suite as well for best results.
Once installed, if you are also installing local genomes, be sure to also install Samtools and create both Samtools and Picard indexes, using Data Managers for all (genome download/install + indexes). Once the tool is functioning/found, it will expect input datasets that are sorted and that have a database metadata attribute assigned.
If there is more troubleshooting to be done, please confirm the Galaxy version, Picard version, and the information that Bjoern requested. Also note if the tool works properly within the Galaxy GUI (through a browser, in a history). If the tool doesn't work there, it will not work line-command.
Thanks! Jen, Galaxy team