HPC/Exascale Centre of Excellence in Personalised Medicine

Sample application

This repository contains a sample application using a single Building Block (BB) within the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) project.

Table of Contents

• HPC/Exascale Centre of Excellence in Personalised Medicine
  • Sample application
  • Table of Contents
  • Repository contents
  • Usage
    • 1^st - Install permedcoe package
    • 2^nd - Download the sample_BB package
    • 3^nd - Set the Singularity image in the sample_BB package
    • 4^nd - Install the sample_BB package
    • 5^rd - Execute one of the sample applications
  • License
  • Contact

Repository contents

• sample_BB: Sample building block (uses the permedcoe package provided by PerMedCoE).
• sample_app: Sample application using sample_BB.

Usage

1^st - Install permedcoe package

git clone https://github.com/PerMedCoE/permedcoe.git
cd permedcoe
./install.sh
cd ..

2^nd - Download the sample_BB package

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

3^nd - Set the Singularity image in the sample_BB package

cd basic_application/sample_BB
# Edit src/sample_BB/main.py
# Set the SAMPLE_CONTAINER variable:
#    It is currently set to: $HOME/github/projects/PerMedCoE/basic_application/sample_BB/image/PerMedCoE-Pilot.sif
#    And that path should be where the PerMedCoE-Pilot.sif file is.

4^nd - Install the sample_BB package

./install.sh
cd ../..

5^rd - Execute one of the sample applications

• PyCOMPSs sample application:

  NOTE: Requires PyCOMPSs installed in the machine.

  cd basic_application/sample_app/PyCOMPSs
  ./launch.sh
  cd ../..

• Nextflow sample application:

  NOTE: Requires Nextflow installed in the machine.

  cd basic_application/sample_app/Nextflow
  ./launch.sh
  cd ../..

• Snakemake sample application:

  NOTE: Requires Snakemake installed in the machine.

  cd basic_application/sample_app/Snakemake
  ./launch.sh
  cd ../..

License

Apache 2.0

Contact

https://permedcoe.eu/contact/