Updating the Pipeline - JoshLoecker/MAPT GitHub Wiki

It may be worthwhile to ensure you have the latest version of the pipeline available by getting the latest changes from GitHub.

1. Navigate to the directory that you cloned the pipeline to
2. Within the pipeline directory, navigate the the setup folder
3. Execute the update_pipeline.sh script by typing: ./update_pipeline.sh
   a. Note the additional ./. This is required.

Caveats

This script saves your config.yaml file by moving it to your home directory, getting the latest changes from GitHub, and moving your config.yaml file back into the directory the update_pipeline.sh script was called from
As a result, any new parameters that may be located in GitHub's config.yaml (and used in the Snakefile), will not be found in your current configuration file.
If you would like to ensure you have the latest changes, including those in config.yaml, perform the following

1. Copy your config.yaml file to your home directory: mv config.yaml ~/config.yaml.backup
2. Update all branches: git fetch --all
3. Reset the current branch: git reset --hard origin/master

Now, open the backup with nano ~/config.yaml.backup and copy your changes to the new file with nano config.yaml.
A better method of ensuring changes do not get overwritten has not been devised as of now.
Please note, changes to config.yaml are not common, and this wil not have to be done frequently.

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