HPO Prerequisites

Installing git and singularity

Please refer to the documentation of the tools for install instructions.

Installing conda

To check if you have conda, use conda --version.

If you do not have conda installed, install with the following commands:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
source ~/.bashrc

Now, using the conda --version command should give the version you’ve downloaded. If not, close the terminal session and open again, then try conda --version.

Installing supervisor

conda create --name IMPROVE python=3.9.16
conda activate IMPROVE
# change to a directory for supervisor if desired
git clone https://github.com/ECP-CANDLE/Supervisor.git
cd Supervisor && export PATH=$PATH:$(pwd)/bin
git checkout develop
pip install numpy deap

Installing swift-t

You need to be in conda environment to proceed. If you aren’t sure:

# Same conda env than above
# conda create --name IMPROVE python=3.9.16
conda activate IMPROVE

Install swift-t via conda. For detailed instructions please refer to the swift-t documentation:

conda install --yes -c conda-forge -c swift-t swift-t

Shared installations

The supervisor tool supports shared installations. For example, a site administrator can install all of the tools above in a public location. The user should be able to run supervisor from a personal directory with all configuration files and output files there.

Setting up a new site

On a simple Linux system, you will simply need to modify
Supervisor/workflows/common/sh/env-local.sh
to specify the software locations on your system.

For more complex systems, you will also need to provide scheduler settings in the sched-SITE.sh script.

See the supervisor tool doc for more details about how to configure a site.