- 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)...
- GN1 github problem
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
- 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...
- 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
...simulated invoking a system command within the `rqtl` script, but the error does not match the observed issue.
## TODO
* [ ] Test in a similar environment to the CD environment to replicate the issue.
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...issue addresses user feedback received during the testing phase of GNQA on CD. The following improvements are required
## Tasks
* [ ] Only show the link when a user is logged in - they can't use it...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...an issue tracker on gemini
Why do we want to consolidate issue trackers and kanban boards using gemini+git? Several reasons:
* Get rid of external web service dependencies (in our case github issue...
- Add an 'Edit Issue' Link to Tissue
✓ issue opened on Mar 24 2022 by Frederick Muriuki Muriithi, last updated on Apr 15 2022 by Arun Isaac
...tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub) editting mode for the selected file.
For an example of what is expected...
- 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...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 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 we have...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...identify
the file in the GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to:
=> https://github.com/genenetwork/genenetwork3/blob/main/gn3/db/genotypes.py
* Linked to issue...
- Zoomed mapping result are empty for certain traits
issue opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
...issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed first in the GEMMA results for a later chromosome.
For example...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR Version.
The root cause of the problem is unclear,
but after reviewing...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...API - so people van validate client side (as a feature).
This mentions RDF - which I think
* aruni
was involved in. I (fredm) have tagged them here, for their evaluation of the relevance of this issue...
- 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...
- 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...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...issue
- [X] Check if database is affected in any way
- [X] Send a patch to fix
- [X] Notify every relevant user
- [X] Update case-attr page with links
## Notes
### Mon 11 Apr 2022 13:19:14 EAT:
The...
- 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
issue opened 8 weeks ago 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...
- 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...