- 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
...zachs
* keywords: bug
* status: in progress
* priority: high
This issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed...
- 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
...UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR Version.
- 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
...Bug
* status: in progress
* keywords: external, qtl, rqtl, bug, logs
## Description
For QTL analysis, we invoke the `rqtl` script as an external process through Python's `subprocess` module.
For...
- 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
...bug
* keywords: collections, from github
## Members
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/559 From GitHub
### Describe the bug
When calcuating principal...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
Make sense?
For the kanban board we can simply use the keywords. Override/add with a separate
* kanban: Brain storm
Keywords are fairly flexible, but common ones are
* request
* bug
* critical bug...
- 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
...Notes
the bug above no longer exists.
gn2 CI runs on the background after for any push
raises an error if any broken link is found
On gn2 web pages all missing links that are found
are underlined...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...bug
* status: closed
* priority: critical
* keywords: critical bug, in progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and click on network...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Variant Browser seems to be using mm9
## Tags
* assigned:
* priority: unclear
* type: bug
* status: stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp...
- Unable to open new tab for mapping/ correlations with Chrome
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 18 2023 by Munyoki Kilyungi
Unable to open new tab for mapping/ correlations with Chrome
## Tags
* assigned: bonfacem
* type: bug
* status: unclear
* priority: medium
* keywords: mapping, correlation, google chrome, UI...
- Search results for SNP looks weird
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Multi-trait heat map failed
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: stalled
* keywords: heatmap, from github
## Members
* zsloan
* pjotrp
* echesler
## Description...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
...bug
* keywords: GN1, genenetwork1, annotation, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID...
- 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
Global search does not close connections properly (and is slow)
## Tags
* type: bug
* priority: medium
* status: stalled
* assigned: Uditgulati
* keywords: global search, db connections, medium...
- 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
...bug
* priority: critical
* keywords: GN1
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating...
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...in rqtl_wrapper.R is wrong. For the time being,
I've removed this option. Currently just waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug...
- 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
correlation error: 'NoneType' object is not iterable
## Tags
* type: bug
* priority: high
* status: closed, completed
* keywords: correlations, from github, high priority
## Description...
- 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
...-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf, pjotrp
* type: bug...
- Return canned text if notebook description returns none
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
## Tags
* type: bug
* assigned: jgart
* priority: high
* status: in progress
* keywords: binderlite, notebooks
## Description
Notebooks that do...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~sircmpwn/antiweb antiweb
Copying nav...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...bug
* priority: critical
* status: unclear
* keywords: correlations, from github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612 From GitHub
> Hi,
>
> There is an...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...bug
* status: unclear
* keywords: CSV, from github, meta data
## Description
=> https://github.com/genenetwork/genenetwork2/issues/594 From GitHub
csv export data can't be read using the example R...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Error when attempt to zoom to a chromosome after mapping a PCA trait
## Tags
* assigned: zsloan
* type: bug
* priority: high
* status: unclear
* keywords: PCA, from github, high...
- 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
It is
used to fire up a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug...
- '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
...bug
* status: closed
* keywords: TempDataSet, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/592 From GitHub
After successful entry of new BXD trait data (both my...
- 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
...bug
* keywords: GN1, genenetwork1, annotation, from github
## Tasks
* [ ] Fix PHP view
* [ ] Fix CKEDITOR
## Description
Turns out that it is a PHP page that is not working. Also CKEDITOR is not...
- 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
...issues may be related to production (i.e. the same). Note also I created my own development VM in just an hour, so I don't have to mess with the fallback while others are using it.
# Tags
* type: bug...