Installation and Usage
How to install and run the workflow
Step 1: Create a virtual environment.
Step 1: For cwltool/toil, please install using python 3.6 as done below:
Here we can use either virtualenv or conda. Here we will use virtualenv.
Once you execute the above command you will see your bash prompt something on these lines:
Step 2: Clone the repository
Step 3: Install requirements using pip
We have already specified the version of cwltool and other packages in the requirements.txt file. Please use this to install.
To see help for the inputs for cwl workflow you can use: cwltool uncollapsed_bam_generation.cwl --help
To see help for the inputs for cwl workflow you can use: toil-cwl-runner uncollapsed_bam_generation.cwl --help
Once we have successfully installed the requirements we can now run the workflow using cwltool/toil if you have proper input file generated either in json or yaml format. Please look at Inputs Description for more details.
Here we show how to use cwltool to run the workflow on single machine
Step 4: Run the workflow with a given set of input using cwltool on single machine
Here we show how to run the workflow using toil-cwl-runner using single machine interface.
Once we have successfully installed the requirements we can now run the workflow using cwltool if you have proper input file generated either in json or yaml format. Please look at Inputs Description for more details.
Step 4: Run the workflow with a given set of input using toil on single machine
Here we show how to run the workflow using toil-cwl-runner on MSKCC internal compute cluster called JUNO which has IBM LSF as a scheduler.
Step 4: Run the workflow with a given set of input using toil on JUNO (MSKCC Research Cluster)
You should now be running the workflow on the specified batch system
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