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genecup is currently running as root on penguin2.

Currently when run using shepherd it fails like this:

guix system: warning: Consider running 'guix pull' followed by

'guix system reconfigure' to get up-to-date packages and security updates.

guile: warning: failed to install locale

Backtrace:

6 (primitive-load "/gnu/store/gkksaranscqwyzixgm4fk83by1n?")

In gnu/build/linux-container.scm:

299:8 5 (call-with-temporary-directory #<procedure 7ff547853640?>)

327:16 4 (_ "/tmp/guix-directory.mkZ75V")

270:12 3 (run-container _ _ (mnt pid ipc uts user) 65536 _ # _ # _)

200:4 2 (initialize-user-namespace _ 65536 #:guest-uid _ # _)

In ice-9/ports.scm:

465:8 1 (call-with-output-file _ _ #:binary _ #:encoding _)

In unknown file:

0 (close-output-port #<output: /proc/15090/uid_map 8>)

ERROR: In procedure close-output-port:

In procedure fport_write: Operation not permitted

A number of changes to different types of shepherd services (exec-command, make-system-constructor) still failed to actually run the container when started with `herd start genecup`. Ratspub is run from a `guix environment` rather than `guix system container` so we'll switch to that so we can go back to running all the services using shepherd.

The commit to make genecup run in a guix environment, using shepherd.

Notes

It is unclear if the environmental-variables in the shepherd service are carried over to the shell script, but it seems not
Had to run 'guix pull' to update the guix tree for genecup, since the guix-bioinformatics repository had made breaking changes since the last time.

genecup is currently running as root on penguin2.

Tags

Notes