Issue Using MIBiG with BiG-SCAPE on Galaxy

usegalaxy.eu support
1

Dear Galaxy Support Team,

I hope you are doing well.

I am experiencing persistent issues while running BiG-SCAPE on Galaxy, specifically related to the inclusion of the MIBiG reference dataset.

:red_circle: MIBiG issue

Whenever I enable the MIBiG option (e.g., --mibig21), the job consistently fails with a read-only filesystem error:

OSError: [Errno 30] Read-only file system:
'/usr/local/lib/python3.7/site-packages/bigscape/Annotated_MIBiG_reference/MIBiG_2.1_final'

As a result, I have not been able to run any analysis with MIBiG included. (Same issue with 3.1 version database)

:white_check_mark: Without MIBiG

When I run BiG-SCAPE without MIBiG, the tool works correctly:

  • I tested inputs as:
    • a collection of region BGC files, and
    • a single combined file (This failed)
  • The analysis completed successfully, indicating that my input files are valid

:warning: Summary of the problem

  • :white_check_mark: Input files → working
  • :white_check_mark: BiG-SCAPE (without MIBiG) → working
  • :cross_mark: Adding MIBiG → always fails

:red_question_mark: Questions

I would appreciate your guidance on the following:

  1. Is there a supported way to run BiG-SCAPE with MIBiG enabled on Galaxy?
  2. Is there a pre-configured/shared MIBiG dataset available to avoid this issue?
  3. Could the tool be adjusted so that MIBiG is extracted or accessed from a user-writable directory instead of the system path?

Including MIBiG is important for my analysis, so having this functionality working would be very helpful.

Thank you very much for your support.

Best regards,
Shreyash