- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Fix GN1 Network Graph
Status: the network graph works on production. PDF output is empty, however.
## Tags
* type: bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban...
- 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
...EC2 URL
* [X] Disable GN mailing list URL
=> ./gn1-pairscan.gmi [x] Pairscan not working
=> ./gn1-network-graph.gmi [X] Fix network graph (it does not display image)
* [ ] Disable all defunct URLs
- 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
...3.741e-05 32.09 4.585 socket.py:938(getaddrinfo)
```
* The above is consistent all the analysis I've done across all the profile dumps.
* Testing my theory out:
```
@app.route("/test-network")...
- 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
...fairly trivial. Next to a pangenome, which is a graph on DNA,
we should present metadata in a structured way (a graph on everything
else).
Metadata and pangenomes ought to go hand in hand
### Describe...
- 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
...GN2 the complexity has increased a lot because of interacting services and a larger dependency graph.
Here I track what it takes today to install a fallback instance of GN2 that is 'frozen' in time.
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them from the file.
Can't think of anything more to add to make it really useful...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...exists)
* [ ] synchronize between queues using a dump
* [ ] sheepdog_expect.rb - expect PINGs
* [ ] sheepdog_rsync.rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 2 weeks ago by Pjotr Prins; 33 of 74 tasks done
.../logs/bnw-server=/var/log --network
ln -s /gnu/store/0hnfb9ynnxsig3yyprwxmg5h6c9g8mry-run-container /usr/local/bin/bnw-app-container
```
systemd service:
```
root@tux02:/etc/systemd/system# cat bnw-app-...
- 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
...-1.3.0-9.f743f20
* [X] set up nginx (Debian)
* [X] test ipmi console
* [X] test ports (nginx)
* [?] set up network for external tux02
* [X] set up deployment evironment
* [X] sheepdog copy database...
- 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...
- 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...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...out with pangenome support.
# Tags
* assigned: pjotrp,zsloan,arthurc,robw
* priority: medium
* type: enhancement
* status: open, in progress
* keywords: mapping, architecture
# TODO
* [ ] Point out...
- 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...
- 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...
- 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...
- 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...
- 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
...(source_url), None)
File "<string>", line 3, in raise_from
urllib3.exceptions.LocationParseError: Failed to parse: http://localhost:8893api/rqtl/compute
```
The error points out a missing slash...