- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...recent call last):
File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1639, in full_dispatch_request
rv = self.dispatch_request()
File...
- 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
...format:
* `content` (the data you want to commit to the file, *valid markdown*)
* `prev_commit` (required for integrity)
* `filename` (file path to the file you are modifying)
* `username` (identifier...
- 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
...835 Apr 2 07:03 -logP.png
```
These are created by the HK run. Harmless for now, but if two people run HK at the same time we'll get a conflict.
Unique file names, but lingering on file system - note...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...File web/images/upload/MouseTissuesRWWMay08.xls is 262.53 MB; this exceeds GitHub's file size limit of 100.00 MB
remote: error: GH001: Large files detected. You may want to try Git Large File Storage...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...csv file for ITP_10001 to add a couple of attributes to it. What I see is that the csv file is somewhat messed up. The values for
Sex, Site, Tx, and Year have shifted down to next row for each sample...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...display an arrow depending on the strand (whether the query strand matches the reference
[ ] Store the homology chain file data differently (keeping it as a text file might be fine, but need to find...
- Adding principal component to collection returns an error
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Alexander Kabui
...last):
File "/usr/local/guix-profiles/gn-latest-20201216/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
rv = self.dispatch_request()
File...
- 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
...stdout in a file.
Args:
cmd: The command to execute, provided as a list of arguments.
output_file: Absolute file path to write the stdout.
run_id: Unique ID to identify the...
- Automatically find broken links on GN2
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 2 of 2 tasks done
...File "/usr/local/guix-profiles/gn-latest-20200513/lib/python2.7/site-packages/flask/app.py", line 1926, in dispatch_request
self.raise_routing_exception(req)
File "/usr/...
- 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...
- 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
...forge's (currently GitHub) editting mode for the selected file.
For an example of what is expected, see the `edit page` link/button at
=> http://gemini.thebird.nl/gemini/genenetwork/gn-gemtext-threads/...
- 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
...I discover that ibdata1 file has grown to 100GB. Not a problem yet, but we should purge that on production at some point
=> https://www.percona.com/blog/2013/08/20/why-is-the-ibdata1-file-continuously-...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...def __init__(self, fd, matrix, traits, imageHtmlName, imageName, pdfName, nodes,
web/webqtl/networkGraph/networkGraphPageBody.py: a <a href="%s" class="normalsize" target="_blank">PDF
file...
- 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
...telling it where the INI file is.
This required adding a path for Apache:
```
SetEnv PHP_INI_SCAN_DIR /home/gn1/production/gnshare/gn-pjotr-test
```
and a php.ini file with
```
[Pdo_mysql]
pdo_mysql...
- 'TempDataSet' object has no attribute 'query_for_group' (error)
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Sep 28 2022 by Alexander_Kabui
...tux01:gene:2.11-rc2-staging-427071fc7 http://www.genenetwork.org/corr_compute (12:29PM UTC Jul 16, 2021)
'TempDataSet' object has no attribute 'query_for_group' (error)
File "/export/local/home/gn2/...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...the genofile 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...
- 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
...show up first in the chromosome 7 result file even if its position is 122Mb. This causes a problem in the mapping display code, since the loop is set to break when the marker position is > the end...
- Global search does not close connections properly (and is slow)
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
...mean
```
2020-08-15 2:53:58 140273206434560 [Warning] Aborted connection 45219 to db: 'db_webqtl' user: 'webqtlout' host: '127.0.0.1' (CLOSE_CONNECTION)
```
generating 6Mb of log file info.
In fact...
- correlation error: 'NoneType' object is not iterable
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 13 2022 by Alexander Kabui
...iterable)
```
GeneNetwork tux01:gene:2.11-rc2-production-283af77a7 http://www.genenetwork.org/corr_compute ( 2:39PM UTC Feb 19, 2020)
'NoneType' object is not iterable (error)
File "/export/local/...
- Using guix-bioinformatics in a channels.scm file
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
...a channels.scm file
channels.scm works fine. Only problem is that we don't have a guix-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...example a BXDPublish phenotype and a phenotype from BXD-LongevityPublish). These mappings could be stored in a simple JSON file.
The "main" group trait(s) could then have their sample data converted...
- CD is slow
issue opened 13 days ago by Pjotr Prins, last updated 9 days ago by Pjotr Prins; 2 of 8 tasks done
...robots.txt file (even though LLMs hardly honour them).
Let's try to get inside the container with nsenter:
```
ps xau|grep genenetwork-development-container
root 115940 0.0 0.0 163692 26296 ?