- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Jun 13 2025 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
* [X] test ports (nginx)
* [?] set up...
- 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...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...py?FormID=sharinginfo&InfoPageName=BXDPublish
Name,Value,SE,N
BXD1,3125.333,803.776,6
BXD2,540.167,448.724,6
```
The metadata need to be commented out and the empty line needs to be removed. R expects...
- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...PID and a recent nsenter:
```
/gnu/store/w7a3frdmffpw3hvxpvvxwxgzfhyqdm6n-profile/bin/nsenter -m -p -t 115961 /run/current-system/profile/bin/bash -login
```
System tools are in '/run/current-system/...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...tied to (updating) reference genomes. Here we track a next generation annotation system which will support versions of annotation with a matching reference genome. In the future we'll build this out...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
.../sdd1 393G 121G 252G 33% /
# swap
/dev/sdd5 partition 976M 76.5M -2
```
We can therefore add four new disks in slots /dev/sdc,sde,sdf,sdh
penguin2 has no out-of-band and no serial connector...
- 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...
- Annotate traits page with metadata from RDF
✓ issue opened on Sep 30 2022 by Munyoki Kilyungi, last updated on Dec 15 2022 by Munyoki Kilyungi; 16 of 16 tasks done
...out if the edits are feasible/important to work on and communicate to PJ/Arun
## Next steps
* [x] Spec out LMDB integration and how it would work out with current statistical operations. Collaborate...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...be stripped out. Here's a current snip of how that looks like:
```
JL00005,896.000000,x,x,896,4/22/04,,4OHPBN_J,Oct,,0^M,M,JL,1,2004
JL00006,1077.000000,x,x,1077,4/22/04,,4OHPBN_J,Apr,,0^M,M,JL,1,2004...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...5.1.6 (cli) (built: Mar 18 2014 20:48:55)
Copyright (c) 1997-2006 The PHP Group
Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies
In guix-bioinformatics we have
```
php 5.6.40 out...
- Capture Data on the BXDs in RDF
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...an ontology exists and it looks sensible we should reuse that. If non-existent, we create our own ontology. Obviously we can't get away from adding free flow textual fields. What we want to lift out...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...file. Though, unlike other issue trackers, this is not obligatory. One can insert notes using the '>' prefix
> This is a comment
Or one can simply use git blame to figure out who did what.
## Closing...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...trait_id=1448231_at&dataset=HC_M2_0606_P
>
> jacs123
I (fredm) tried this out, and it seems there is still an issue here.
This appears to no longer be an issue; it was probably addressed along...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 11 days 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...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Commenting
out functionality
Reverting on that code still won't show the image contained in
```
<img border="0" alt="the graph" src="/image/tmpzmtq88.gif" usemap="#webqtlGraph" />
```
The interesting...
- 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...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...AND ProbeSetFreeze.public > 0 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name LIMIT 600;
```
To find out what index is problematic we first look at sizes. Tables...
- 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
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
..."Central nervous system, behavior, learning and memory: Morris water maze search-time preference, amount of time spent in the trained quadrant of the pool minus mean time in the alternative quadrants...
- 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...