IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click
here
created by Tiffany_at_Broad
on 2017-12-01
- Within the Method Repository, click on the Create New method... button
- Upon creation, you will be prompted to enter the following information:
- Namespace: the "folder" where you want to store this method. Frequently analysts use their name, lab name, or institution name. Read more about namespaces here.
- Name: the desired name of this method
- Synopsis (optional): a description of this method
- Documentation (optional): any markdown formatted text that you want to add to describe this method. You can put copyright information here, versions of software/tools used in the Docker image, or any details that are important.
- Copy/paste your WDL into the WDL text block or click "Load from file..." to load a WDL file from your computer.
- Snapshot comment (optional): add notes about what changes were made between snapshots here (like git commits)
Using the Command Line interface
The FireCloud Command Line Interface (CLI) provides another option to upload methods (WDL) to the Method Repository.
- Download the FireCloud Command Line Interface. You can also run a Docker version without downloading to your local environment.
- Enter
cd firecloud-cli in your Terminal to change directories. - Enter the FireCloud CLI push command. The box below shows an example of a command you use to push a method.
firecloud -u [https://api.firecloud.org/api](https://api.firecloud.org/api) -m push -t Workflow -s broad-firecloud-jn-test -n test-method -y 'Test synopsis' file.wdl - You will see a "Successfully pushed" message indicating your method uploaded to FireCloud. You can also confirm your Method pushed by viewing the Method Repository. If your push failed, you will see an error message. To troubleshoot, please share the error message in the Forum.
Description of CLI Commands
- Enter -u, then state the URL of the FireCloud environment.
- Enter -m, then state the command (push).
- Enter -t, then state Workflow as the type for pushing your Method.
- Enter -s, then state the Method Namespace.
- Enter -n, then state the Method name.
- Enter -y, then describe your Method
- Finally, enter the file name for your WDL.
Updated on 2018-05-04