Installation and Usage

You must have run the Nucleo workflow first before running any of the MSK-ACCESS QC workflows. Depending on your use case, there are two main sets of workflows you can choose to run: (1) `qc_generator

Step 1: Create a virtual environment.

Option (A) - if using cwltool

If you are using cwltool only, please proceed using python 3.6 as done below:

Here we can use either virtualenv or conda. Here we will use virtualenv.

python3-virtualenv

pip3 install virtualenv
python3 -m venv my_project
source my_project/bin/activate

Option (B) - recommended for Juno HPC cluster

If you are using toil, python 3 is required. Please install using Python 3.6 as done below:

Here we can use either virtualenv or conda. Here we will use virtualenv.

python3-virtaulenv

pip install virtualenv
virtualenv my_project
source my_project/bin/activate

Once you execute the above command you will see your bash prompt something on this lines:

bash-prompt-example

(my_project)[server]$

Step 2: Clone the repository

git-clone-with-submodule

git clone --recursive --branch 0.1.0 https://github.com/msk-access/access_qc_generation.git

Note: Change 0.1.0 to the latest stable release of the pipeline

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.

python-package-installation-using-pip

#python3
pip3 install -r requirements.txt

Step 4: Generate an inputs file

Next you must generate a proper input file in either json or yaml format.

For details on how to create this file, please follow this example (there is a minimal example of what needs to be filled in at the end of the page):

Inputs Description

It's also possible to create and fill in a "template" inputs file using this command:

$ cwltool --make-template nucleo.cwl > inputs.yaml

Note: To see help for the inputs for cwl workflow you can use: toil-cwl-runner nucleo.cwl --help

Once we have successfully installed the requirements we can now run the workflow using cwltool/toil .

Step 5: Run the workflow

Using cwltool

Here we show how to use cwltool to run the workflow on a single machine, such as a laptop

Run the workflow with a given set of input using cwltool on single machine

To generate the QC files for one sample:

cwltool-execution

cwltool nucleo.cwl inputs.yaml

Using toil-cwl-runner locally

Using toil-cwl-runner on JUNO

Your workflow should now be running on the specified batch system. See outputs for a description of the resulting files when is it completed.