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@@ -80,3 +80,62 @@ With that knowledge, we can now get a shell using ~nsenter~ as follows: which will give you a bash shell with the ~PATH~ environment variable setup correctly to give you access to all packages in the global profile. + +* Troubleshooting Tips + +** Use Profiles + +When troubleshooting, we need to be using the correct profile that has all the necessary dependencies. Use a [[https://ci.genenetwork.org/channels.scm][channels]] file to set up a profile. An example of a channel that was fixed at Python 3.9: + +#+begin_src scheme +(list (channel + (name 'gn-bioinformatics) + (url "https://gitlab.com/genenetwork/guix-bioinformatics") + (branch "master") + (commit + "9939feb61ea29881d42628bc58a43886f7da6573")) + (channel + (name 'guix-forge) + (url "https://git.systemreboot.net/guix-forge/") + (branch "main") + (introduction + (make-channel-introduction + "0432e37b20dd678a02efee21adf0b9525a670310" + (openpgp-fingerprint + "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3"))))) +#+end_src + +Activate a profile by: + +#+begin_src bash +export GUIX_PROFILE=~/.guix-extra-profiles/genenetwork +. $GUIX_PROFILE/etc/profile +#+end_src + +Double-check to confirm that you are using the correct channel using =guix describe=. The use of profiles is well documented [[https://issues.genenetwork.org/topics/guix-profiles][here]]---it should match your channels.scm file. + +** View Logs + +When troubleshooting our containers, all our log files are located in "/export2/guix-containers/genenetwork-development/var/log": + +#+begin_src sh +tail /export2/guix-containers/genenetwork-development/var/log/cd/genenetwork2.log +tail /export2/guix-containers/genenetwork-development/var/log/cd/genenetwork3.log +#+end_src + +Note that to be able to view log files, you have to have root permissions. + +** Back-ups + +When running borg, you can run into the following error: + +#+begin_src text +root@tux02:/export3/local/home/bonfacem# borg list /export3/backup/tux01/borg/borg-tux01/ +Cache, or information obtained from the security directory is newer than repository - this is either an attack or unsafe (multiple repos with same ID) +#+end_src + +To fix it: + +: borg config repo id +: rm ~/.config/borg/security/REPO_ID/manifest-timestamp +: borg delete --cache-only REPO |