tissue issue tracker

issue opened on Dec 17 2022 by Pjotr Prins

...system administration
* keywords: systems, tux02, production, gn1
# Info
To solve this I have to remove the large file(s). Fortunately not many people are using genenetwork1 code base, so I can...

Each shepherd service needs its own guix profile.

issue opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins

...(genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug
* status: in progress
* priority: high
* keywords: shepherd, system administration

Tux02 Production

issue opened on Oct 07 2021 by Pjotr Prins, last updated on Dec 14 2022 by Pjotr Prins; 17 of 22 tasks done

...system administration
* keywords: systems, tux02, production
## Tasks
* [X] update guix guix-1.3.0-9.f743f20
* [X] set up nginx (Debian)
* [X] test ipmi console (172.23.30.40)
* [X] test ports (nginx)...

GN2 Time Machines

issue opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done

...system administration
* keywords: systems, production
## Tasks
Also a time line:
* [X] Install machine software and physical (est. 4-8 hours)
* [X] Sync backups on a daily basis and add monitoring (2...

Apps

issue opened on Nov 19 2024 by Pjotr Prins, last updated 7 weeks ago by Pjotr Prins; 33 of 74 tasks done

...BNW
The app is already a Guix system container! To make it part of the startup I had to move it away from shepherd (which runs in userland) and:
```
/home/shepherd/guix-profiles/bnw/bin/guix system...

Tux01 hard disk crash

issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi

...system, tux01, hard disk crash
# Info
The system is still up, so it is not too urgent. First step is to recover the backup system. The rsync backups are in an inconsistent state, fortunately...

Fallbacks and backups

issue opened on Aug 31 2021 by Pjotr Prins, last updated on Jun 28 2024 by Pjotr Prins; 3 of 25 tasks done

...//sheepdog.genenetwork.org/sheepdog/index.html
See also
=> /topics/systems/restore-backups Restore Backups
## Tags
* type: enhancement
* assigned: pjotrp
* keywords: systems, fallback, backup, deploy...

Fallback issues

issue opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done

.../systems/debug-and-developing-code-with-genenetwork-system-container.gmi
That way I was able to troubleshoot the paths and added them to the containers.
## QTLReaper showing font problem (fixed)
Try HK...

Sheepdog

issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done

...system, sheepdog
## Tasks
* [X] add locking functionality for tags - added borg with-lock (test)
* [X] chgrp functionality in sheepdog_borg
* [ ] check whether rsync dir exists, repo valid and/or no...

GN1 Production

issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done

Penguin2 RAID 5

in progress

issue opened on Feb 28 2025 by Pjotr Prins

Annotation

issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done

Annotation
Annotation, assembly and liftover are recurring themes because they are tied to (updating) reference genomes. Here we track a next generation annotation system which will support versions...

AI UI Enhancements

issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done

...our GPT [GNQA system] <- button
Showing 1 to 69 of 1,210 entries
Index Record Species Group Tissue Dataset Symbol ...
table entries...
```
So suggest it as an option when continueing global search.

Investigate and Fix `rm` Command in `rqtl` Logs

issue opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done

...arguments (i.e., no direct string injection).
* [x] The subprocess is not invoked within a shell environment, which would otherwise result in string injection.
* [x] We simulated invoking a system...

GN Markdown Editor Integration

issue opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done

...with HTMX
* [x] Support external links and image rendering
* [x] Package dependencies
* [x] show diff for files
* [x] Handle errors
* [ ] Review by users
* [x] Integrate authentication into the system...