Usage without VM

[timeu]

We have a managed galaxy service which is connected to our HPC system. Some users showed interest in using the PiRATE pipeline. As a workaround we started the VM but we want to run the pipeline on our managed Galaxy service. Provided that all software dependencies are installed, what would be necessary to replicate the VM ? Do I just need to copy the tools-conf.ini and the tools xmls ?

[JBerthelier]

Dear timeu, Thank you for your interest about PiRATE and sorry for my delay, In case ever sofware dependenses are installed, you can probably replicate the pipeline. But I don't advise you to do that because it could be time consuming because of numerous xml are configurated according to the VM. In particularly with REPET dependencies (TEdenovo, PASTEC and TEannot). You might need to re-configure their .config files, MySQL db in the xml. I hope my answer will help you.

Best regards, Jeremy