github.com/ENCODE-DCC/long-read-rna-pipeline/long-read-rna-pipeline

Automatic Tools and Workflows
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This is a companion discussion topic for the original entry at github.com/ENCODE-DCC/long-read-rna-pipeline/long-read-rna-pipeline
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IMPORTANT:
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 https://github.com/ENCODE-DCC/long-read-rna-pipeline

  • 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 github.com/ENCODE-DCC/long-read-rna-pipeline/long-read-rna-pipeline:PIP-1619-dockstore --json Dockstore.json --config .dockstore/config
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No need to do this anymore. We made the docker image a workflow input, so now everything should work out of box.