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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
BSD 3-Clause "New" or "Revised" License
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No 00-buildGeneFile.R file in broad_sanger #167

Closed coleslaw481 closed 1 month ago

coleslaw481 commented 1 month ago

I was trying to follow this readme: https://github.com/PNNL-CompBio/coderdata/blob/main/build/broad_sanger/README.md

and on the first step, the 2nd command:

docker run -v $PWD:/tmp/ broad_sanger Rscript 00-buildGeneFile.R

expects 00-buildGeneFile.R file, but it is not found and I get this error:

docker run -v $PWD:/tmp/ broad_sanger Rscript 00-buildGeneFile.R
Fatal error: cannot open file '00-buildGeneFile.R': No such file or directory

thanks,

chris

sgosline commented 1 month ago

Yes, this was moved to the genes docker, try using the build script