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bioinform / neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
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split_bed.py errors #11

Closed AllenAkhaumere closed 6 years ago

AllenAkhaumere commented 6 years ago

I'm having issues working with the split_bed source code. raise NotImplementedError(help_str) NotImplementedError: "sortBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method. I installed the recent version of BEDTools but the problem persist. Any idea what the issues might be?

msahraeian commented 6 years ago

@AllenAkhaumere happy to see your interest in NeuSomatic. This error usually happens when bedtools bin folder is not in your PATH. You can check that by which sortBed.
If it is missing from PATH you can export it as: export PATH="/PATH/TO/bedtools2/bin:$PATH".

I would recommend to use anaconda (or miniconda) as explained here to install all the python packages. Then you should make sure the conda binary folder is in your PATH by export PATH="/PATH/TO/anconda/bin:$PATH".

AllenAkhaumere commented 6 years ago

OK