vincent-noel/UC2Workflow

Use Case 2 Workflow - Drug synergies on cell lines

Use Case 2 Workflow

This folder contains all needed for the Use Case 2 Workflow : Drug synergies on cell lines.

• Use Case 2 Workflow
  • Contents
    • Building Blocks
    • Workflows
    • Resources
  • Instructions
    • Local machine
      • Requirements
      • Usage steps
    • MareNostrum 4
      • Requirements in MN4
      • Usage steps in MN4
  • License
  • Contact

Contents

Building Blocks

The uc2_BBs folder contains the Building Blocks used in the UC2 Workflow.

Workflows

The uc2_workflow folder contains the workflows implementations.

Currently contains only the implementation using PyCOMPSs.

Resources

The resources folder contains the building blocks assets and images, and a small dataset.

Instructions

Local machine

This section explains the requirements and usage for the COVID19 Pilot workflow in a laptop or desktop computer.

Requirements

• permedcoe package
• PyCOMPSs
• Singularity

Usage steps

1. Clone this repository

2. Install the uc2_BBs package

   cd covid19_BBs && ./install.sh && cd ..

3. Go to uc2_workflow/PyCOMPSs folder

4. Execute ./run.sh

The execution is prepared to use the singularity images that must be placed into resources/images folder (MaBoSS.sif, PhysiCell-COVID19.sif and single_cell.sif), the assets folder located into resources/assets and the dataset located into resources/data.

⚠️ WARNING: The singularity containers need to be downloaded from the project B2DROP.

TIP: If you want to run the workflow with a different dataset, please place the dataset into resources/data and update the run.sh script according to the dataset name.

MareNostrum 4

This section explains the requirements and usage for the COVID19 Pilot workflow in the MareNostrum 4 supercomputer.

Requirements in MN4

• Access to MN4

All requirements are already installed in MN4.

Usage steps in MN4

1. Load the COMPSs and permedcoe modules

   export COMPSS_PYTHON_VERSION=3-ML
   module load COMPSs/2.9
   module load singularity/3.5.2
   module use /apps/modules/modulefiles/tools/COMPSs/libraries
   module load permedcoe

   TIP: Include the loading into yout ${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 (COVID19_BB_IMAGES environment variable), assets (COVID19_BB_ASSETS environment variable) and testing dataset (COVID19_PILOT_DATASET environment variable).

   TIP: It also provides an alias to ease the access to resources: goto_covid19pilotresources

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

   cd desired_folder
   get_covid19pilotworkflow

3. Go to covid19_pilot_workflow/PyCOMPSs folder

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 COVID19_BB_IMAGES environment variable). It uses the assets located into the COVID19_BB_ASSETS environment variable and dataset located into COVID19_PILOT_DATASET environment variable.

⚠️ TIP: If you want to run the workflow with a different dataset, please override the COVID19_PILOT_DATASET environment variable (or update the dataset variable into the launch.sh script) with your desired dataset path.

License

Apache 2.0

Contact

https://permedcoe.eu/contact/