longr/biobb-wf-md-setup-protein-cwl

BioExcel CWL example simulation system

Introduction

Common Workflow Language example that illustrates the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

Requirements

• CWLtool
• Docker
• Git
• Git Submodules

Instructions for installing both of these are available on the linked websites.

Getting started

Setup

Make sure you have git, Docker and cwltool installed. If you are not familiar with CWL you can see the user guide here

Obtaining the files

This example requires the BioBB libraries. To make it easier to find and access these they are included in the directory biobb @ xxxxxxx through use of git submodules. This means that you cannot download a zip and must clone the repository instead.

To clone the repository and setup the submodules, you need to do the following three setps:

1. Clone the repository to the machine you want to use it on.
2. Change into that directory
3. Initialise the submodules, which downloads the required submodules to the machine.

These steps can be done with the following commands:

git clone [email protected]:bioexcel/biobb-wf-md-setup-protein-cwl.git
cd biobb-wf-md-setup-protein-cwl
git submodule update --init

You can also clone the repository and initialise the submodules in one command:

git clone --recurse-submodules [email protected]:bioexcel/biobb-wf-md-setup-protein-cwl.git
cd biobb-wf-md-setup-protein-cwl

Usage

Before running the simulation, make sure that docker is running and installed.

There are two parts to this example (or any CWL example): The workflow file, which describes the workflow, and the input file which specifies the inputs,outputs and other configurable options.

• protein_md.cwl is the workflwo file.
• protein_md_input_description.yml is the input or configuration file.

To run the simulation use the command:

cwltool protein_md.cwl protein_md_input_descriptions.yml

All inputs will be downloaded as the simulation is carried out.

This workflow takes around 30 minutes to 1 hour to run on a quad-core Intel i5 processor.

Outputs

Whilst this is running a lot of output will be printed to the screen. The final part will list all of the output files created and it should then say:

Final process status is success

Copyright & Licensing

This software has been developed in the eScience Lab and Research IT groups at the University of Manchester as part of BioExcel

Licensed under the Apache License 2.0, see the file LICENSE for details.