This is a companion discussion topic for the original entry at github.com/ENCODE-DCC/long-read-rna-pipeline/long-read-rna-pipeline
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:
In dockstore configuration file
long-read-rna-pipeline/.dockstore/configreplace 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
For example the complete launch command to run the pipeline from branch
PIP-1619-dockstoreafter the addition would then be:
dockstore workflow launch --entry github.com/ENCODE-DCC/long-read-rna-pipeline/long-read-rna-pipeline:PIP-1619-dockstore --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.