First install MambaForge (conda will work too but MambaForge is much faster at solving dependencies)
If you decide to use conda replace all
mamba references with
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" bash Mambaforge-$(uname)-$(uname -m).sh
Create a new mamba/conda environmenht
mamba create -n playmolecule mamba activate playmolecule mamba install python=3.10 ipython -c conda-forge
You can then pip install the PlayMolecule with
pip install playmolecule
Then add the following to your
.bashrc file with the path provided by your administrator
Acellera will provide you with a license file for the applications and a Google service account JSON file. The administrator has to perform a few extra steps to completed the PlayMolecule installation for the users.
Install the license file or license server
Install the applications over Google Cloud
If you are intending to run the applications on more than a single machine you will need to setup a license server. For more information on how to set up a license server (Floating license) please see https://software.acellera.com/acemd/licence.html#licence-server
Otherwise just place the license file on a location where all users can access it on the single machine.
To install the applications for the users you need to follow these steps:
Install Google Cloud CLI to authenticate with Google Cloud where the app images are stored. Installation instructions can be found here: https://cloud.google.com/sdk/docs/install
gcloud initstep of the above instructions authenticate with any account you wish.
Install the following pip packages in addition to
playmolecule which are needed for the admin installation.
pip install playmolecule questionary google-cloud-storage==1.35.0 tqdm
Choose a path where PlayMolecule will be installed. If you are running the applications in a cluster like SLURM
choose a path which is accessible from all machines (i.e. on a shared file system).
Otherwise choose a path on your local machine which is accessible to all users on that machine.
Set up the path in your
.bashrc file as follows:
To create the PlayMolecule installation open an ipython console and type the following:
from playmolecule import update_apps
This will start an interactive installation of PlayMolecule to guide you through setting up everything. At some step it will ask you for the service account JSON file which Acellera has provided you with for downloading the applications.
Later if you want to update the applications again to their latest versions you can run the following commands:
from playmolecule import update_apps update_apps()