Welcome to MSK-ACCESS help documents

MSK-ACCESS workflows came into existence because of the need to write flexible, portable and easy to use tools.

MSK-ACCESS workflows features

  1. Containers : Using docker to host tool images to be used by Common Workflow Language
  2. Common Workflow Language (CWL) : Have commandline tools written in common workflow language specification.
  3. Workflow of workflow : We will join multiple CWL workflows togather to create a final workflow.

Pipeline Diagram

Installing package

Here is how to install these tools without sudo rights:

Please replace workflow with repo containing the workflow of your interest

curl -LO https://github.com/msk-access/workflow/archive/master.zip
unzip workflow-master.zip
cd workflow-master
python setup.py install --user

Add this to your ~/.bash_profile to get access to the *.cwl tools:

# Set PATH to include local python bin if found
if [ -d "$HOME/.local/bin" ]; then
    PATH="$HOME/.local/bin:$PATH"
fi