Cancer Invasion Workflow

Table of Contents

• Cancer Invasion Workflow
  • Table of Contents
  • Description
  • Contents
    • Building Blocks
    • Workflows
    • Resources
    • Tests
  • Instructions
    • Local machine
      • Requirements
      • Usage steps
    • MareNostrum 4
      • Requirements in MN4
      • Usage steps in MN4
    • Mahti or Puhti
      • Requirements
      • Steps
  • License
  • Contact

Description

Uses multiscale simulations to describe cancer progression into invasion.

The workflow uses the following building blocks, described in order of execution:

1. PhysiBoSS-Invasion

For details on individual workflow steps, see the user documentation for each building block.

GitHub repository

Contents

Building Blocks

The BuildingBlocks folder contains the script to install the Building Blocks used in the Cancer Invasion Workflow.

Workflows

The Workflow folder contains the workflows implementations.

Currently contains the implementation using PyCOMPSs and Snakemake (in progress).

Resources

The Resources folder contains dataset files.

Tests

The Tests folder contains the scripts that run each Building Block used in the workflow for the given small dataset. They can be executed individually for testing purposes.

Instructions

Local machine

This section explains the requirements and usage for the Cancer Invasion Workflow in a laptop or desktop computer.

Requirements

• permedcoe package
• PyCOMPSs / Snakemake
• Singularity

Usage steps

1. Clone this repository:

git clone https://github.com/PerMedCoE/cancer-invasion-workflow

2. Install the Building Blocks required for the Cancer Invasion Workflow:

cancer-invasion-workflow/BuildingBlocks/./install_BBs.sh

3. Get the required Building Block images from the project B2DROP:

• Required images:
  • PhysiCell-Invasion.singularity

The path where these files are stored MUST be exported in the PERMEDCOE_IMAGES environment variable.

:warning: TIP: These containers can be built manually as follows (be patient since some of them may take some time):

1. Clone the BuildingBlocks repository

   git clone https://github.com/PerMedCoE/BuildingBlocks.git
   

2. Build the required Building Block images

   cd BuildingBlocks/Resources/images
   sudo singularity build PhysiCell-Invasion.sif PhysiCell-Invasion.singularity
   cd ../../..
   

If using PyCOMPSs in local PC (make sure that PyCOMPSs in installed):

4. Go to Workflow/PyCOMPSs folder

   cd Workflows/PyCOMPSs
   

5. Execute ./run.sh

If using Snakemake in local PC (make sure that SnakeMake is installed):

4. Go to Workflow/SnakeMake folder

   cd Workflows/SnakeMake
   

5. Execute ./run.sh

TIP: If you want to run the workflow with a different dataset, please update the run.sh script setting the dataset variable to the new dataset folder and their file names.

MareNostrum 4

This section explains the requirements and usage for the Cancer Invasion Workflow in the MareNostrum 4 supercomputer.

Requirements in MN4

• Access to MN4

All Building Blocks are already installed in MN4, and the Cancer Invasion Workflow available.

Usage steps in MN4

1. Load the COMPSs, Singularity and permedcoe modules

   export COMPSS_PYTHON_VERSION=3
   module load COMPSs/3.1
   module load singularity/3.5.2
   module use /apps/modules/modulefiles/tools/COMPSs/libraries
   module load permedcoe
   

   TIP: Include the loading into your ${HOME}/.bashrc file to load it automatically on the session start.

   This commands will load COMPSs and the permedcoe package which provides all necessary dependencies, as well as the path to the singularity container images (PERMEDCOE_IMAGES environment variable) and testing dataset (CANCERINVASIONWORKFLOW_DATASET environment variable).

2. Get a copy of the pilot workflow into your desired folder

   mkdir desired_folder
   cd desired_folder
   get_cancerinvasionworkflow
   

3. Go to Workflow/PyCOMPSs folder

   cd Workflow/PyCOMPSs
   

4. Execute ./launch.sh

This command will launch a job into the job queuing system (SLURM) requesting 2 nodes (one node acting half master and half worker, and other full worker node) for 20 minutes, and is prepared to use the singularity images that are already deployed in MN4 (located into the PERMEDCOE_IMAGES environment variable). It uses the dataset located into ../../Resources/data folder.

:warning: TIP: If you want to run the workflow with a different dataset, please edit the launch.sh script and define the appropriate dataset path.

After the execution, a results folder will be available with with Cancer Invasion Workflow results.

Mahti or Puhti

This section explains how to run the Cancer Invasion workflow on CSC supercomputers using SnakeMake.

Requirements

• Install snakemake (or check if there is a version installed using module spider snakemake)
• Install workflow, using the same steps as for the local machine. With the exception that containers have to be built elsewhere.

Steps

1. Go to Workflow/SnakeMake folder

   cd Workflow/SnakeMake
   

2. Edit launch.sh with the correct partition, account, and resource specifications.

3. Execute ./launch.sh

:warning: Snakemake provides a --cluster flag, but this functionality should be avoided as it's really not suited for HPC systems.

License

Apache 2.0

Contact

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).