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Utility Scripts

Sometimes we need to run some utility scripts manually to set up certain things that do not render themselves to automation very well.

This is especially relevant for any script that might need to interact with the SQLite database.

This document notes some gotchas that you might run into trying to run

Register System Administrator

Start by getting a shell into the CI/CD container:

sudo guix container exec <PID> /run/current-system/profile/bin/bash --login

replacing =<PID>= with the process ID of the container.

Now stop GN3:

herd stop genenetwork3

In a separate terminal on the *host* system, change the owner of the directory and file:

sudo chown -R fredm /export/data/genenetwork-sqlite

Now start a guix shell in the *genenetwork3* repository (on the host) and run the utility script(s) you need to run:

$ cd /home/fredm/genenetwork3
$ guix shell --container --network --share=/export/data/genenetwork-sqlite \
    --development --file=guix.scm
[env] $ python3 -m scripts.register_sys_admin \

Once you have run (all) the utility script(s) you needed to run, you can exit the shell and restore the file user:

sudo chown -R guixbuilder13 /export/data/genenetwork-sqlite

now go back to the CI/CD container shell and restart genenetwork3:

herd start genenetwork3

then exit the shell.

Failed Attempts


mount --bind -o rw,umask=0002,gid=1000,uid=1000 \
    /home/frederick/genenetwork/local-ci-cd/data/genenetwork-sqlite \

but the file (and mount target) retain the original permissions.

(made with skribilo)