This is a template repository for Singularity/Dockerfile containers/images and build scripts
If you use this material for scientific publications, please cite it as follows:
Espen Hagen, Bayram Cevdet Akdeniz, Alexandr Frei. (2022). precimed/container_template: container_template-0.1.0rc0 (v0.1.0rc0). Zenodo. https://doi.org/10.5281/zenodo.7244728
To use these codes, do not clone or fork this repository, but click the green Use this template button above.
You may then create a new repository on a GitHub organization or user account (<user>) under a new project name (<project>),
that can be cloned by issuing in a terminal application
git clone git@github.com:<user>/<project>.git
cd <project>
The codes may then be adapted further to suit the requirements of the project, as described next
After cloning the template repository as described above a few requirements must be in place. Some scripts rely on Python with some packages available in the Python environment.
One convenient way to set up a Python environment is Conda, available via Miniconda or Miniforge.
Assuming one of these Python distributions is installed, issue the following to create a new Python environment using conda:
conda create -n <container_template> python=3 pip # create environment named <container_template>
conda activate <container_template> # activates enviromnent <container_template>
pip install -r setup-requirements.txt
To set up your own project from this template, issue in the terminal:
python scripts/init.py
The script is interactive, and will prompt the user for some info.
It will modify certain files in the <project> directory and also replace this README file.
Some files may also be renamed.
Remember to commit and push the changes after running the setup script (scripts/init.py):
git add <file1> <file2> ...
git commit -m "initial setup"
git push
The remaining codes may then be added to and be modified further to suit the requirements of the <project>.
See the updated project README.md file for further instructions.