I was able to fix the dependency issues by running lsof +D /[path-to-deps] which indicated some PIDs of python that were using the .nfs file.
After killing those I was able to finish the install process. However, now when I run jobs, I see this error in cryosparcm joblog:
Traceback (most recent call last): File "<string>", line 1, in <module> ModuleNotFoundError: No module named 'cryosparc_compute.run'
This may be related to my attempts at following the steps listed in this post