Work has been done to remove dependency on hard-coded paths, however the interface of some applications (sgEvolver) is most simply configured if its dependent binaries are on PATH.
If we do this for one, we might as well assume this as a requirement for all pipeline executables.
Currently we have Bash and Python scripts in a binary folder, and use relative references.
bin/
pbsrun_XXX.sh
makeTruth.py
Instead, we should probably put all dependent executables (samtools, bwa, sgEvolver) in or beneath this path, then add this to PATH or use an new environmental variable. Probably a new one, then that is already implemented for adding to PATH if desired.
Work has been done to remove dependency on hard-coded paths, however the interface of some applications (sgEvolver) is most simply configured if its dependent binaries are on PATH.
If we do this for one, we might as well assume this as a requirement for all pipeline executables.
Currently we have Bash and Python scripts in a binary folder, and use relative references.
Instead, we should probably put all dependent executables (samtools, bwa, sgEvolver) in or beneath this path, then add this to PATH or use an new environmental variable. Probably a new one, then that is already implemented for adding to PATH if desired.