- 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...
- CD is slow
issue opened 13 days ago by Pjotr Prins, last updated 9 days ago by Pjotr Prins; 2 of 8 tasks done
...Consortium M430v2 (Jun06) PDNN 1457545_at 9530036O11Rik long non-coding RNA, expressed sequence tag (EST) AK035474 with high bladder expression antisense EST 14 Kb upstream of Shh...
- 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...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...priority: high
* type: bug
* status: unclear
* keywords: CSV, from github, meta data
## Description
=> https://github.com/genenetwork/genenetwork2/issues/594 From GitHub
csv export data can't...
- 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
...Data on the BXDs in RDF
## Tags
* assigned: bonfacem, pjotrp, zsloan
* priority: high
* status: unclear
* type: feature-request, enhancement
* keywords: RDF, BXD, REST, from github, high priority...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Jul 26 2023 by Alexander_Kabui; 2 of 6 tasks done
...priority: high
* status: in progress
## Notes
having identified ways to link genofiles to Dataset
and fetching sample data and case attributes using them
we need to integrate the components intoa...
- '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
'TempDataSet' object has no attribute 'query_for_group' (error)
## Tags
* assigned: alex
* priority: high
* type: bug
* status: closed
* keywords: TempDataSet, from github
## Description...
- 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
Adding principal component to collection returns an error
## Tags
* assigned: alex
* status: unclear
* priority: high
* type: bug
* keywords: collections, from github
## Members
* rupertoverall...
- 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
...priority: high
* status: in progress
* keywords: rdf, critical, metadata
Read the design-doc here:
=> /topics/add-metadata-to-trait-page
This task is related to:
=> /issues/capture-data-on-BXDs-...
- Fetch trait data using genofiles
issue opened on Jul 11 2023 by Alexander_Kabui, last updated on Jul 13 2023 by Alexander_Kabui; 2 of 3 tasks done
...improvement
* priority: high
* status: in progress
## Notes
since Genenetwork database does not have all genotype files when fetching sample data use genotypes to fetch trat data given a dataset...
- 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
...alexm
* status: in progress
* priority: high
* tags: markdown, integration, guile
## Notes
This is a to-do list to integrate the GN Markdown editor into GN2.
To see the implementation, see:
=> https...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...alexm
* type: debug
* priority: high
* status: in progress
## Notes
A dataset can have multiple groups. In order to fetch all possible sample data fetch all possible groups in a dataset then use...
- 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
...priority: high
* status: closed, completed
* keywords: correlations, from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/374 From GitHub
Dear Developer...
- 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 priority...
- 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
...bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug
* status: in progress
* priority: high...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the Submit Trait feature only allows for trait data (submitted as just a string...
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...Alex, SoloShelby
* Priority: High
* Type: LLM
* Keywords: LLM
* Status: In Progress
# Description
There are discrepancies when asking questions on Qnqa using Fahamu. Sometimes, responses take too...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...alexm
* type: debug
* priority: high
* status: in progress
## Once you identify the genofile identify
the file in the GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to...
- 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
...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 first in the GEMMA results for a later...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
GN1 annotation page broken
## Tags
* assigned: zsloan, pjotrp
* priority: high
* status: overdue
* type: bug
* keywords: GN1, genenetwork1, annotation, from github
## Description...
- 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
...alexm, zsloan
* Priority: high
* status: in progress
* Keyword : search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser versions.
This...
- 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...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Currently you can't do an analysis beween traits from the "main" BXD group...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...download that data for use, they were not being stripped out. As a consequence, opening the csv file in Excel (or similar) software resulted in data that seems jumbled up.
### Tue 12 Apr 2022 13:33:31...
- 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
...expected, see the `edit page` link/button at
=> http://gemini.thebird.nl/gemini/genenetwork/gn-gemtext-threads/topics/data-uploads/editing-data.gmi
noting how it drops you straight into editting the...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...and footers
* + [ ] Create portal page
* + [ ] Show specific datasets
* + [ ] Show specific publications
* + [ ] Show specific twitter feed
# Tags
* assigned: pjotrp
* type: feature
* priority: high...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419 From GitHub
These queries take 3 minutes...
- 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...
- 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
...backups
* [ ] mount bacchus on HPC
## Backup and restore
We are using borg for backing up data. Borg is excellent at deduplication and compression of data and is pretty fast too. Incremental copies...
- 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
...caches data and index pages. MyISAM only caches index pages.
Just in this area alone, MyISAM does not waste time caching data. That's because it's not designed to cache data. InnoDB caches every data...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...trimmed_values)
IndexError: reaper: the length of the strain list and the value list are different,
```
One of my traits had missing data, deselecting this trait fixed the problem. Record 20761.
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...data as CSV via the web interface includes the following header information:
```
Record ID,10620
Symbol,WMZTrgtQuadTime
Description,"Central nervous system, behavior, learning and memory: Morris water...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...hash can be computed over data that is streamed over the REST API - so people van validate client side (as a feature).
This mentions RDF - which I think
* aruni
was involved in. I (fredm) have tagged...
- 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
...hard to also enable for other species)
[ ] Make it display an arrow depending on the strand (whether the query strand matches the reference
[ ] Store the homology chain file data differently (keeping...
- 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
...pjotrp
* priority: high
* status: testing
* type: bug
* keywords: GN1, genenetwork1, annotation, from github
## Tasks
* [ ] Fix PHP view
* [ ] Fix CKEDITOR
## Description
Turns out that it is a PHP...
- 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
.../mysql/data/mysqld.pid
+# ExecStartPost=/bin/sh -c "systemctl unset-environment _WSREP_START_POSITION"
-ExecStartPost=/etc/mysql/debian-start
+RestartSec=15s
+TimeoutStartSec=infinity
+TimeoutStopSec...
- 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
...search does not close connections properly (and is slow)
## Tags
* type: bug
* priority: medium
* status: stalled
* assigned: Uditgulati
* keywords: global search, db connections, medium priority...
- 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...
- Tux01 hard disk crash
issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...crash
One spinning disk crashed on Sept. 26th. It was used for Arthur's HOME and backups.
# Tags
* assigned: pjotrp
* priority: medium
* status: in progress
* keywords: system, tux01, hard disk crash...
- 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
...looks weird
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395...
- Redirect Users to the Correct URL on Login for GN2
✓ issue opened on Sep 17 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
Redirect Users to the Correct URL on Login for GN2
## Tags
* assigned: alexm
* priority: medium
* status: in progress
* keywords: gn-auth, auth, redirect, login, completed, closed, done...
- 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
...Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug
* assigned: zsloan, danny
* status: in progress, halted
* keywords: marker covariates
* priority...
- 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
...move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf, pjotrp
* type: bug
* keywords: guix-bioinformatics
* status: in progress
* priority: medium
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~sircmpwn/antiweb antiweb
Copying nav bar...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...zsloan
* type: bug
* priority: critical
* status: unclear
* keywords: correlations, from github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612 From GitHub
> Hi...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...priority: medium
* type: refactor
* status: open, in progress
* keywords: tables, javascript
# Description
Currently most DataTables are drawn independently, so each separate page has its own...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...versions of annotation with a matching reference genome. In the future we'll build this out with pangenome support.
# Tags
* assigned: pjotrp,zsloan,arthurc,robw
* priority: medium
* type: enhancement...
- 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
Automatically find broken links on GN2
## Tags
* assigned: zsloan, alex
* type: bug
* priority: medium
* status: completed, closed
* keywords: GN1, GN2, broken links, from github
## Members
* Millak...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated 7 weeks ago by Pjotr Prins; 17 of 22 tasks done
...solid. The idea is to have 4-6 times a year upgrades. Also we should be able to roll back on an upgrade and be able to create time machines.
## Tags
* assigned: pjotrp
* status: in progress
* priority...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated on Mar 23 2025 by Pjotr Prins; 33 of 74 tasks done
...priority: medium
* keywords: system, sheepdog, shepherd
# Tasks
* [ ] Get services running
* [ ] Move guix shell into containers
* [ ] Make sure the container starts up on reboot and/or migrate...
- 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
...priority: critical
# Tasks
* [X] 502 timeout errors
* [X] Rqtl2 not working
* [X] 413 error
* [ ] BNW error
* [ ] Monitor service - both systemd and sheepdog
* [ ] Files in /tmp
## 502 timeout...