Majiq and Voila command builder tool

[Paul Jewell]

Good afternoon Majiq users. 

Due to some internal popular demand, I have recently created a small web application with some good examples for compiling the required inputs (config file and commandline) for majiq + voila analysis. This interactive yet simple tool will guide you to a good starting point for running many common analysis types supported by our tools, and make compiling the commands much less tedious for you!

Please feel free to provide feedback on this thread or another as you see fit, and let us know if the tool proves helpful in getting started with using majiq and voila tools!

The tool can be found on our documentation site here: https://biociphers.bitbucket.io/majiq/command_builder.html

Thanks and have an awesome day, 

-Paul

[Julian Rozenberg]

Dear Paul,

Thank you very much for creating this beautiful tool

However, I got problems running it!!!

I suppose, this is because we still have an outdated version 2.1-179b437 ?

I was trying to build a config file using you online tool and I am getting this message:

Please advise what I have to do?

Shall I first try to get a new version?

Thank you very much

Sincerey.

Julian Rozenberg PhD.

Senior Scientist 

Laboratory of the Molecular Oncology

Moscow Institute of Physics and Technology

/nas/longleaf/apps/majiq/2.0/lib/python3.5/site-packages/majiq/src/config.py:68: UserWarning: bamdirs parameter not found in config file, using "./" instead

  warnings.warn('bamdirs parameter not found in config file, using "./" instead')

/nas/longleaf/apps/majiq/2.0/lib/python3.5/site-packages/majiq/src/config.py:74: UserWarning: sjdirs parameter not found in config file, using "./" instead

  warnings.warn('sjdirs parameter not found in config file, using "./" instead')

Traceback (most recent call last):

  File "/nas/longleaf/apps/majiq/2.0/bin/majiq", line 11, in <module>

    load_entry_point('majiq==2.1', 'console_scripts', 'majiq')()

  File "/nas/longleaf/apps/majiq/2.0/lib/python3.5/site-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 "/nas/longleaf/apps/majiq/2.0/lib/python3.5/site-packages/majiq/src/basic_pipeline.py", line 11, in pipeline_run

    return pipeline.run()

  File "majiq/src/build.pyx", line 529, in majiq.src.build.Builder.run

  File "/nas/longleaf/apps/majiq/2.0/lib/python3.5/site-packages/majiq/src/config.py", line 30, in __new__

    Config.instance = Config.__Config(*argv)

  File "/nas/longleaf/apps/majiq/2.0/lib/python3.5/site-packages/majiq/src/config.py", line 77, in __init__

    self.genome = general['genome']

KeyError: 'genome'