Config file .ini file not being recognised using Singularity.

[Ben J Draper]

Hi,

I'm using Singularity (similar to docker) to use a MAJIQ image. I believe everything is formatted correctly and I wrote absolute paths to all file locations but I can't seem to correctly implement the build function.

Here in the workshop example:

singularity exec /pathto/majiq.img majiq build -c settings.ini DB.gff3 -o /pathto/workshop_example/

Here is the error:

Traceback (most recent call last):
  File "/usr/local/bin/majiq", line 11, in <module>
    load_entry_point('majiq==2.1', 'console_scripts', 'majiq')()
  File "/usr/local/lib/python3.6/dist-packages/majiq/run_majiq.py", line 204, in main
    args.func(args)
  File "majiq/src/build.pyx", line 520, in majiq.src.build.build
  File "/usr/local/lib/python3.6/dist-packages/majiq/src/basic_pipeline.py", line 11, in pipeline_run
    return pipeline.run()
  File "majiq/src/build.pyx", line 528, in majiq.src.build.Builder.run
RuntimeError: Config file settings.ini does not exist

My suspicion is that it has something to do with using Singularity so I'm going to try it locally. Any help would be much appreciated.

Many thanks

Ben J Draper

[Paul Jewell]

Hello Ben,

Could you humor me and try first to put the absolute paths to settings.ini as well as DB.gff3?  For example,

singularity exec /pathto/majiq.img majiq build -c /pathto/settings.ini /pathto/DB.gff3 -o /pathto/workshop_example/

?