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lanagarmire / SSrGE

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Name inconsistency between config and scripts #2

Open FarzanT opened 5 years ago

FarzanT commented 5 years ago

Hello, I have found the following name inconsistency causing the garmire_SNV_calling/deploy_star.py to fail:

Traceback (most recent call last):
  File "garmire_SNV_calling/deploy_star.py", line 20, in <module>
    from garmire_SNV_calling.config import OUTPUT_PATH
ImportError: cannot import name OUTPUT_PATH

I believe the issue is the difference between https://github.com/lanagarmire/SSrGE/blob/f05ac55f609e4d4618288b5d29c064f021ceffcb/garmire_SNV_calling/deploy_star.py#L20 and https://github.com/lanagarmire/SSrGE/blob/f05ac55f609e4d4618288b5d29c064f021ceffcb/garmire_SNV_calling/config.py#L109

Please have a look. Thank you

FarzanT commented 5 years ago

Apparently the issue arrises in https://github.com/lanagarmire/SSrGE/blob/f05ac55f609e4d4618288b5d29c064f021ceffcb/garmire_SNV_calling/process_multiple_snv.py#L17