This is a companion discussion topic for the original entry at

The automatically generated launch command (in “Launch” tab on the right hand side of the “Info” tab on this page) does not work. The following modifications are needed:

  • Clone

  • In dockstore configuration file long-read-rna-pipeline/.dockstore/config replace the placeholder [ABSOLUTE-PATH-TO] with the actual absolute path to the long-read-rna-pipeline github repo.

  • Add to the automatically generated launch command options --config .dockstore/config
    For example the complete launch command to run the pipeline from branch PIP-1619-dockstore after the addition would then be:

dockstore workflow launch --entry --json Dockstore.json --config .dockstore/config

No need to do this anymore. We made the docker image a workflow input, so now everything should work out of box.