/singularity-conda-template

Primary LanguageShell

Template Singularity Conda environment

Setup Instructions

  1. Copy this repository and upload to https://gitlab.nci.org.au/bom/ngm to be able to use gitlab-ci, e.g.

    git clone git@git.nci.org.au:bom/ngm/modules/singularity-conda-template $MYENV
cd $MYENV
git push --set-upstream git@git.nci.org.au:bom/ngm/modules/$MYENV master

  2. Set up environment.yaml with the Conda packages you wish to use

  3. In build.sh update COMMANDS to the list of commands to expose to the user

Manual Build

Build the container manually by running:

./submit.sh

This will submit a job on copyq, with the image available with:

module use /scratch/$PROJECT/$USER/ngm/modules
module load $NAME/$VERSION

Name will be by default the name of this directory, and version the current git branch name.

CI Build

If the repository is under https://git.nci.org.au/bom/ngm/modules then CI will automatically build the image when the repository is updated. The module will be available with:

module use /scratch/hc46/hc46_gitlab/ngm/modules
module load $NAME/$VERSION

Name will be by default the name of the repository, and version the current git branch name.