Greetings to the team! As a long time cryosparc user, on both an HPC cluster and a personal workstation, I was surprised to bump into installation issues recently. I tried to run an install from scratch of the latest cryosparc (4.6.2), and the installer kept failing partway through. I eventually traced this to install.sh (cryosparc_master) lines 354,390-391. The second two lines are new since the last time I installed cryosparc from scratch (several years ago, version 3 or even 2):
eval $(./bin/cryosparcm env)
…
if [[ $PATH =~ (^|:)"${ROOT_DIR}/bin"(:|$) ]] ; then
echo " cryosparc bin directory already in PATH, skipped."
The first line causes the installer to set the PATH variable to include cryosparc executables. The second two lines seem intended to skip the bashrc setup if the PATH variable already includes the cryosparc executables.
Of course, because of the first line, the new if statement always evaluates to true, even when the user PATH did not previously point to cryosparc’s directories. At least in my hands, the installer subsequently chokes and fails to finish.
This is in standalone mode (I am aware of new cluster options, but have only begun to explore them). I can’t see how this script would ever work successfully, but maybe I am missing something?
The workaround was easy enough (I pre-modified the .bashrc to include the needed path to cryosparc binaries); but it did cost me significant time to figure out, and I wonder whether other users have encountered this?