Skip to content

README.md

Latest commit

 

History

History
100 lines (71 loc) · 2.8 KB

README.md

File metadata and controls

100 lines (71 loc) · 2.8 KB
Raw

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

Repository contents

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

Usage

1st - Install permedcoe package

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

2nd - Download the sample_BB package

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

3nd - 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.

4nd - Install the sample_BB package

./install.sh
cd ../..

5rd - 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/