Pre-process tutorial file not working

calico / basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

Apache License 2.0

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Pre-process tutorial file not working #181

Closed riapai closed 10 months ago

riapai commented 11 months ago

The issue is occurring in /basenji/tutorials/preprocess.ipynb. In line 4:! basenji_data.py -s .1 -g data/unmap_macro.bed -l 131072 --local -o data/heart_l131k -p 8 -t .1 -v .1 -w 128 data/hg19.ml.fa data/heart_wigs.txt There is no data/file generated in data/heart_l131k. Because of this the rest of the tutorial cannot be completed.

rubensolozabal commented 11 months ago

Hi, it works to me, you just need to change the paths, e.g. basenji_data.py - > bin/basenji_data.py. Same for data paths.

davek44 commented 10 months ago

Yes, you have to specify the path or add the bin/ directory to your $PATH variable, which I recommend in the README.