Building and Running the SPARCED Singularity Container¶
This section explains how to build and interact with the SPARCED Singularity container for deploying and running the SPARCED pipeline.
Building the Container¶
To build the SPARCED Singularity container, follow these steps:
1. Prerequisites¶
Ensure you have Singularity installed on your system. You can check by running:
`bash singularity --version `If not installed, refer to the [Singularity Installation Guide](https://sylabs.io/guides/) for detailed instructions.
2. Clone the SPARCED Repository¶
Clone the repository to your local machine:
`bash git clone https://github.com/JonahRileyHuggins/SPARCED.git cd SPARCED `
3. Build the Container¶
Use the following command to build the container from the provided definition file:
`bash singularity build --fakeroot container/sparced.sif container/sparced.def `This will create the sparced.sif file in the container/ directory.Note: Ensure the SPARCED/ directory does not include unnecessary files (e.g., .git) by excluding them in the definition file or using a cleanup process.
** Running or Shelling into the Container**
1. Shell into the Container¶
To access an interactive shell within the container:
`bash singularity shell container/sparced.sif `This drops you into the container environment where you can navigate and run commands.Example Command:
`bash sparced -h `
2. Run the Container Directly¶
To execute the default command defined in the container (e.g., running sparced):
`bash singularity run container/sparced.sif `
3. Bind Directories (Optional)¶
To ensure the container can read/write files on your host system, use the –bind flag:
`bash singularity shell --bind /path/to/SPARCED:/SPARCED container/sparced.sif `This binds the SPARCED directory on your host to the container, allowing full access during execution.
4. Execute Specific Commands¶
Use the exec command to run specific commands in the container:
`bash singularity exec container/sparced.sif sparced compile -n Basic_model `This runs the sparced tool directly inside the container.
Tips - Use –cleanenv if you want to isolate the container environment from your host machine’s variables. - Always verify permissions for bound directories to ensure proper read/write access.
For additional support or troubleshooting, refer to the [Singularity Documentation](https://apptainer.org/user-docs/2.5/index.html).