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DevelopingHCP / structural-pipeline

dHCP structural pipeline
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Error during additional pipeline #1

Closed chrisk1 closed 6 years ago

chrisk1 commented 7 years ago

The pipeline fails during the additional pipeline stage, due to a path error. Running on Ubuntu 14.04 with a local installation, but processing files located in an sshfs-mounted remote drive. Tracing it back, there is a problem with:

parameters/configuration.sh, line 4 export parameters_dir=$(dirname "$BASH_SOURCE")

where $(dirname "$BASH_SOURCE") resolves to ./parameters and hence the rest fails, as this isn't a complete path.

Replacing this line with a hard-coded path allows the script to run to completion: export parameters_dir=/home/username/structural-pipeline/parameters

A universal solution (from https://stackoverflow.com/a/246128/1518749), that seems to work perfectly here is: export parameters_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

Hope that helps!

amakropoulos commented 6 years ago

Thanks Chris, this is now fixed as you describe!