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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.
=> https://git.genenetwork.org/efraim/shepherd-services/commit/b3c96077c2ae3ebda05eb53d81fa6e377a55132d 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.
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