Issue running the example

ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions

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Issue running the example #20

Closed radaniba closed 8 years ago

radaniba commented 8 years ago

Hello Breakmer dev

I am trying to run the example provided in the repo, after personalizing the brakmer.cfg I tried running the do as below, but got that isue

python breakmer.py example_data/breakmer.cfg
usage: breakmer.py [options]
breakmer.py: error: argument fncCmd: invalid choice: 'example_data/breakmer.cfg' (choose from 'run', 'start_blat_server', 'prepare_reference_data')

Anything you missed in the doc maybe ?

mducar commented 8 years ago

Hi,

It looks like you left out the "run" from the command line. I assume by the other ticket you opened you already resolved this one?

radaniba commented 8 years ago

Yes you're right.

I think you need to update the readme file as well as I just tried to follow your recommendation at first place.

Thanks for getting back to me