Broken pipe during update to v4.0.1

Install, Configure and Update
1

Hi there,

My connection was broken during the update to v4.0.1, during the “Extraction…” step of the update. Now, when I use any of the cryosparcm commands, I receive the following error:

Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress

I see that the solution from the website appears to just be a fresh install of cryoSPARC, but I’m wondering if there’s any alternative. Additionally, it seems that my license information is missing, as echo $LICENSE_ID returns nothing, and I see the following message when I run cryosparcm status:

(base) [zahodnbd@em504-02 ~]$ cryosparcm status

Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress

----------------------------------------------------------------------------

CryoSPARC System master node installed at

/ibex/scratch/projects/c2030/cryosparc/cryosparc_master

Current cryoSPARC version: v4.0.1

----------------------------------------------------------------------------

/ibex/scratch/projects/c2030/cryosparc/cryosparc_master/bin/cryosparcm: line 1215: supervisorctl: command not found

CryoSPARC process status:

----------------------------------------------------------------------------

Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress

An error ocurred while checking license status

Could not get license verification status. Are all CryoSPARC processes RUNNING?

Any help is appreciated!

2

I also recommend a fresh installation, and a record of the screen output when you run the
install.sh command(s).

I am not sure what effect an active conda environment may have on CryoSPARC installation and maintenance. You may want to conda deactivate before you re-attempt installation.

Please ensure that you define the LICENSE_ID variable in the shell in which you will run the installation:
export LICENSE_ID="<license_id>"
(substitute your actual license id)
and confirm that
echo $LICENSE_ID
prints your actual license id to the screen before you run the
./install.sh --license $LICENSE_ID .. command(s).
After ./install.sh .. for master and worker are completed successfully, the license id will be stored by the CRYOSPARC_LICENSE_ID variables inside the cryosparc_master/config.sh and cryosparc_worker/config.sh files, repectively. LICENSE_ID will then no longer be needed.

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