Cryosparc is a data processing pipeline installed on athena. It runs via a web interface.

Because it uses a web interface, it has its own user (cryosparc) on the server, and the data files are read and written as that user. This can cause permission problems.

The easiest way to fix these permission problems is to log in as cryosparc, and mount your files from frodo or athena via sshfs. The Cryosparc web server can then write files on frodo as you.

To log in as cryosparc, send me your ssh keys, and I will add them to the cryosparc account.

ssh cryosparc@athena

After you do that, you are on athena, as cryosparc. From there, you
  first check to see if you are already mounted (the usual case) :-
mount
mount


  You should see, near the bottom, this :-

username@frodo:/data/USER001 on /home/cryosparc/username001 type fuse.sshfs (rw,nosuid,nodev,relatime,user_id=1001,group_id=1001)athena:/data/T0024936 on /home/WF/t0024936/athena type fuse.sshfs (rw,nosuid,nodev,relatime,user_id=1221825586,group_id=1767200513)

If you see that - you are ready for work. If you do not see that,
  mount your frodo files, like this :-

mkdir username # make a directory to hold your mountsshfs username@frodo:/data/USER001 username # mount your data on frodo

frodo

Then you can type mount again, and re-check.
 

You need to add yourself as a "user" for cryosparc - which has its own user management (as it has to run from the web interface).

As the cryosparc user, type this :-

cryosparcm createuser --email <yourlogin@uct.ac.za> --password S3CR3T --name "Sipho Monesi"

You only need to do this once.