Modifying the Container Script

Oct 13, 2025 by pynkocean.com 65 views

Introduction

Apptainer, formerly known as Singularity, is a popular containerization platform that allows users to create and manage isolated environments for their applications. When installing Apptainer, users may encounter errors related to missing files or directories. In this article, we will focus on resolving the 'pathway-tools-28.0-linux-64-tier1-install' not found error that occurs during the installation process.

Understanding the Error

The error message indicates that the container script is looking for a file called pathway-tools-28.0-linux-64-tier1-install but is unable to find it. This file is likely a dependency required for the installation of Apptainer. The error message also mentions that the file is not found in the specified location, which is /pmn.

Identifying the Issue

Upon closer inspection, it appears that the file pathway-tools-28.0-linux-64-tier1-install is not present in the current directory. However, there is a file called pathway-tools-28.5-linux-64-tier1-install that is available. This suggests that the container script is looking for a specific version of the pathway-tools package, which is not available in the current directory.

Resolving the Issue

To resolve this issue, we need to ensure that the correct version of the pathway-tools package is available in the current directory. Since the file pathway-tools-28.5-linux-64-tier1-install is available, we can try to use this version instead of the missing pathway-tools-28.0-linux-64-tier1-install version.

Modifying the Container Script

To modify the container script, we need to update the pmn.sh file to use the correct version of the pathway-tools package. We can do this by editing the pmn.sh file and updating the PATHWAY_TOOLS_VERSION variable to point to the correct version of the package.

# Edit the pmn.sh file
$ nano pmn.sh

Update the PATHWAY_TOOLS_VERSION variable to point to the correct version of the package:

# Update the PATHWAY_TOOLS_VERSION variable
PATHWAY_TOOLS_VERSION="pathway-tools-28.5-linux-64-tier1-install"

Rebuilding the Apptainer Container

After modifying the container script, we need to rebuild the Apptainer container using the updated pmn.sh file. We can do this by running the following command:

$ SINGULARITY=apptainer ./pmn.sh build

This will rebuild the Apptainer container using the correct version of the pathway-tools package.

Conclusion

In this article, we resolved the 'pathway-tools-28.0-linux-64-tier1-install' not found error that occurred during the installation of Apptainer. We identified the issue as a missing file and updated the container script to use the correct version of the pathway-tools package. By following the steps outlined in this article, users should be able to resolve this error and successfully install Apptainer.

Troubleshooting Tips

Make sure that the correct version of the pathway-tools package is available in the current directory.
Update the pmn.sh file to use the correct version of the pathway-tools package.
Rebuild the Apptainer container using the updated pmn.sh file.

Additional Resources

Apptainer documentation: https://apptainer.org/docs/
Apptainer community forum: https://discourse.apptainer.org/

FAQs

Q: What is the cause of the 'pathway-tools-28.0-linux-64-tier1-install' not found error? A: The error is caused by a missing file or directory required for the installation of Apptainer.
Q: How do I resolve the 'pathway-tools-28.0-linux-64-tier1-install' not found error? A: Update the container script to use the correct version of the pathway-tools package and rebuild the Apptainer container.
Apptainer Installation FAQs =============================

Q: What is Apptainer?

A: Apptainer is a popular containerization platform that allows users to create and manage isolated environments for their applications. It is a powerful tool for developers, researchers, and scientists who need to run complex applications in a controlled and reproducible environment.

Q: What is the difference between Apptainer and Docker?

A: Apptainer and Docker are both containerization platforms, but they have some key differences. Apptainer is designed to be more secure and flexible than Docker, with features such as support for multiple container runtimes and a more robust security model. Apptainer is also designed to be more compatible with HPC (High-Performance Computing) environments.

Q: How do I install Apptainer on my system?

A: To install Apptainer on your system, you will need to follow the installation instructions for your specific operating system. You can find the installation instructions on the Apptainer website.

Q: What are the system requirements for Apptainer?

A: The system requirements for Apptainer vary depending on the specific use case and the size of the container. However, in general, Apptainer requires a 64-bit operating system and a minimum of 4 GB of RAM.

Q: How do I create a new Apptainer container?

A: To create a new Apptainer container, you will need to create a new file called apptainer.def that defines the container's configuration. You can then use the apptainer build command to build the container.

Q: How do I run an Apptainer container?

A: To run an Apptainer container, you will need to use the apptainer run command. You can specify the name of the container and any additional options as needed.

Q: How do I manage Apptainer containers?

A: Apptainer provides a number of tools for managing containers, including the apptainer ps command for listing running containers and the apptainer rm command for removing containers.

Q: What are the benefits of using Apptainer?

A: Apptainer provides a number of benefits, including improved security, flexibility, and compatibility with HPC environments. It also provides a more robust security model and support for multiple container runtimes.

Q: What are the limitations of Apptainer?

A: Apptainer has a number of limitations, including a steeper learning curve than some other containerization platforms. It also requires a 64-bit operating system and a minimum of 4 GB of RAM.

Q: How do I troubleshoot Apptainer issues?

A: To troubleshoot Apptainer issues, you can use the apptainer logs command to view the container's logs and the apptainer debug command to enable debug mode.

Q: What are some common Apptainer errors?

A: Some common Apptainer errors include the "pathway-tools-28.0-linux-64-tier1-install" not found error, which can be resolved by updating the container script to use the correct version of the pathway-tools package.

Q: How do I get help with Apptainer?

A: You can get help with Apptainer by visiting the Apptainer website, where you can find documentation, tutorials, and a community forum. You can also contact the Apptainer support team directly for assistance.

Q: What are some resources for learning Apptainer?

A: Some resources for learning Apptainer include the Apptainer documentation, tutorials, and a community forum. You can also find online courses and training programs that cover Apptainer.

Q: How do I contribute to the Apptainer community?

A: You can contribute to the Apptainer community by participating in the community forum, submitting bug reports, and contributing to the Apptainer codebase. You can also help to promote Apptainer by sharing your experiences and knowledge with others.