github.com/ENCODE-DCC/rna-seq-pipeline/rna-seq-pipeline

Automatic Tools and Workflows
1
This is a companion discussion topic for the original entry at github.com/ENCODE-DCC/rna-seq-pipeline/rna-seq-pipeline
2

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/rna-seq-pipeline

  • In dockstore configuration file rna-seq-pipeline/.dockstore/config replace the placeholder [ABSOLUTE-PATH-TO] with the actual absolute path to the rna-seq-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-1618-dockstore after the addition would then be:

dockstore workflow launch --entry github.com/ENCODE-DCC/rna-seq-pipeline/rna-seq-pipeline:PIP-1618-dockstore --json Dockstore.json --config .dockstore/config