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.

• assigned: Efraim
• type: failure
• keywords: genecup, penguin2
• status: closed
• priority: high

• 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.