setup.sh and activate.sh do not work completely
so, I used the "setup.sh" and "activate.sh" and the pipeline would not run. It complained about not finding tdqm
after some poking around it turns out the problems is that the conda installation doesn't work. I used my old conda installation. I went back to my /nas/clivings directory, and used "$ source .bashrc" command to remind my linux partition to actually look in my .bashrc file, which tells it where my old installation of conda is then I used "conda activate /nas/clivings/..../python-venv" and, viola!, conda opened that environment and, voila!, the pipeline runs.
SO
my diganosis is: the setup.sh isn't installing conda in a useful way. Or at least, it isn't modifying the .bashrc file and then the activate.sh is not reminding the linux environment to use the modified .bashrc file.
BUT
the conda environment created by the setup.sh DOES work (so far)