RefChef comes with two commands:
RefChef requires a
In addition to the
refchef-menu commands, RefChef requires a
master.yaml containing a list of references, indices, annotations, and metadata, as well as the commands necessary to download and process the files.
refchef-cook is executed, RefChef will append the
master.yaml to change the
complete option from
trueand will also add a
uuid for each reference, the date the files were downloaded and their location, as well as a complete list of files downloaded.
Based on the arguments you pass to
refchef-cook, it will either commit those changes to
master.yaml to a local repository or commit and push the changes to a remote repository.
RefChef requires configuration information:
- Where you'd like the references to be saved
- The local git repository for version control of references
- The remote github repository for version control of reference sequences (optional).