[Bug] Paths Swapped In Singularity Example

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Introduction

In this article, we will discuss a bug that was encountered while running the assembly.py script with Singularity. The bug was caused by the paths being swapped in the export PATH statement, leading to an error message complaining about being unable to find "Sys/Hostname.pm in @INC". We will explore the issue, provide a solution, and discuss the importance of updating the walkthrough to prevent similar issues in the future.

Describe the Bug

When running the assembly.py script with Singularity, the following error message was encountered:

...
SINGULARITY_IMAGE="containers/veba_assembly.sif"
SINGULARITY_CMD="export PATH=/usr/bin:/opt/conda/bin; export CONDA_PREFIX=/opt/conda; \
               assembly.py -1 ${READ_1} -2 ${READ_2} \
               -n ${NAME} -o ${OUTPUT_DIRECTORY}"

singularity exec \
    --bind "${LOCAL_WORKING_DIRECTORY}:${CONTAINER_WORKING_DIRECTORY}" \
           "${SINGULARITY_IMAGE}" bash -c "${SINGULARITY_CMD}"

The error message was complaining about being unable to find "Sys/Hostname.pm in @INC". This error occurred after the 1__assembly step, during the 2__alignment step. The full error message was not available, but a screenshot of the relevant message was provided.

Cause of the Bug

After digging around, it was discovered that the issue was caused by the fact that /usr/bin/perl was being found before /opt/conda/bin/perl in the export PATH statement. This was causing the Perl module "Sys/Hostname.pm" to be loaded from the wrong location, leading to the error message.

Solution

To fix the issue, the order of the paths in the export PATH statement was swapped. The corrected statement is as follows:

...
# works
SINGULARITY_CMD="export PATH=/opt/conda/bin:/usr/bin; export CONDA_PREFIX=/opt/conda; \
               assembly.py -1 ${READ_1} -2 ${READ_2} \
               -n ${NAME} -o ${OUTPUT_DIRECTORY}"

...

By swapping the order of the paths, the Perl module "Sys/Hostname.pm" was loaded from the correct location, and the error message was resolved.

Versions

The following versions were used to reproduce the bug:

  • Singularity version: 3.5.3
  • Docker image of veba_assembly: 2.4.0

Conclusion

In conclusion, the bug was caused by the paths being swapped in the export PATH statement, leading to an error message complaining about being unable to find "Sys/Hostname.pm in @INC". The solution was to swap the order of the paths, and the corrected statement was updated in the walkthrough to prevent similar issues in the future.

Recommendations

To prevent similar issues in the future, it is recommended to:

  • Always check the order of the paths in the export PATH statement.
  • Verify that the Perl module "Sys/Hostname.pm" is loaded from the correct location.
  • Update the walkthrough to reflect the corrected statement.

By following these recommendations, users can avoid encountering similar issues and ensure that their scripts run smoothly.

Future Work

In the future, it would be beneficial to:

  • Investigate the root cause of the issue and provide a more permanent solution.
  • Update the documentation to reflect the corrected statement.
  • Provide additional testing to ensure that the corrected statement works in all scenarios.

By addressing these areas, users can have confidence in the stability and reliability of the script.

Additional Information

For more information on the walkthrough and the corrected statement, please refer to the following resources:

Introduction

In our previous article, we discussed a bug that was encountered while running the assembly.py script with Singularity. The bug was caused by the paths being swapped in the export PATH statement, leading to an error message complaining about being unable to find "Sys/Hostname.pm in @INC". In this article, we will provide a Q&A section to address common questions and concerns related to the bug and its solution.

Q: What is the cause of the bug?

A: The bug was caused by the fact that /usr/bin/perl was being found before /opt/conda/bin/perl in the export PATH statement. This was causing the Perl module "Sys/Hostname.pm" to be loaded from the wrong location, leading to the error message.

Q: How do I fix the bug?

A: To fix the bug, you need to swap the order of the paths in the export PATH statement. The corrected statement is as follows:

...
# works
SINGULARITY_CMD="export PATH=/opt/conda/bin:/usr/bin; export CONDA_PREFIX=/opt/conda; \
               assembly.py -1 ${READ_1} -2 ${READ_2} \
               -n ${NAME} -o ${OUTPUT_DIRECTORY}"

...

Q: What versions of Singularity and veba_assembly were used to reproduce the bug?

A: The following versions were used to reproduce the bug:

  • Singularity version: 3.5.3
  • Docker image of veba_assembly: 2.4.0

Q: How can I prevent similar issues in the future?

A: To prevent similar issues in the future, you can follow these recommendations:

  • Always check the order of the paths in the export PATH statement.
  • Verify that the Perl module "Sys/Hostname.pm" is loaded from the correct location.
  • Update the walkthrough to reflect the corrected statement.

Q: What are the benefits of updating the walkthrough?

A: Updating the walkthrough to reflect the corrected statement provides several benefits, including:

  • Ensuring that users have the most up-to-date information.
  • Preventing similar issues in the future.
  • Improving the overall user experience.

Q: Can I use this solution with other versions of Singularity and veba_assembly?

A: While the solution was tested with Singularity version 3.5.3 and veba_assembly version 2.4.0, it may work with other versions as well. However, it is recommended to test the solution with your specific version of Singularity and veba_assembly to ensure compatibility.

Q: Where can I find more information on the walkthrough and the corrected statement?

A: For more information on the walkthrough and the corrected statement, please refer to the following resources:

Q: Can I contribute to the walkthrough and provide feedback on the solution?

A: Yes, you can contribute to the walkthrough and provide feedback on the solution. Please submit a pull request or open an issue on the GitHub repository to provide your feedback and suggestions.

Conclusion

In conclusion, the Q&A section provides a comprehensive overview of the bug and its solution. By following the recommendations and testing the solution with your specific version of Singularity and veba_assembly, you can ensure that your scripts run smoothly and efficiently.