diff --git a/README.md b/README.md index 591750d..95dc358 100644 --- a/README.md +++ b/README.md @@ -1,44 +1,5 @@ This project allows to use singularity containers transparently on HPCs, so that an application inside the container can be used without adjusting any scripts or pipelines (e.g. nipype). -## Important: add bind points to .bashrc before executing this script -This script expects that you have adjusted the Singularity Bindpoints in your .bashrc, e.g.: -``` -export SINGULARITY_BINDPATH="/gpfs1/,/QRISdata,/data" -``` +_Information on the **Neurodesk** project is available at [neurodesk.github.io](https://neurodesk.github.io)_ -## This gives you a list of all tested images available in neurodesk: -https://github.com/NeuroDesk/neurodesk/blob/master/cvmfs/log.txt -``` -curl -s https://raw.githubusercontent.com/NeuroDesk/neurodesk/master/cvmfs/log.txt -``` - -## Clone repo into a folder with the intented image name -``` -git clone https://github.com/NeuroDesk/transparent-singularity convert3d_1.0.0_20210104 -``` - -## Install -This will create scripts for every binary in the container located in the $DEPLOY_PATH inside the container. It will also create activate and deactivate scripts and module files for lmod (https://lmod.readthedocs.io/en/latest/) -``` -cd convert3d_1.0.0_20210104 -./run_transparent_singularity.sh convert3d_1.0.0_20210104 -``` - -# Use in module system LMOD -Add the module folder path to $MODULEPATH - -# Manual activation and deactivation (in case module system is not available). This will add the paths to the .bashrc -## Activate -``` -source activate_convert3d_1.0.0_20210104.sh -``` - -## Deactivate -``` -source deactivate_convert3d_1.0.0_20210104.sif.sh -``` - -## Uninstall container and cleanup -``` -./ts_uninstall.sh -``` +_Information on **Transparent Singularity** is available at [neurodesk.github.io/developers/transparent_singularity](https://neurodesk.github.io/developers/transparent_singularity)_