- Pin Channel Commits; Decouple from Guix
✓ issue opened on Nov 03 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi; 4 of 5 tasks done
...guix: Mainline Guix channel
* guix-past: Channel for old packages, no longer maintained on guix mainline
* guix-rust-past-crates: Channel for rust packages using the old packaging form
* guix-forge...
- Failing Services' Startup
✓ issue opened on Aug 20 2025 by Frederick Muriuki Muriithi, last updated on Nov 11 2025 by Munyoki Kilyungi
.../home/bonfacem/.guix-ext…")
In guix/ui.scm:
2399:7 15 (run-guix . _)
2362:10 14 (run-guix-command _ . _)
In ice-9/boot-9.scm:
1752:10 13 (with-exception-handler _ _ #:unwind? _ # _)
In guix/...
- Guix CI failure: guix-past build breaks due to missing (libchop)
✓ issue opened on Nov 11 2025 by Munyoki Kilyungi, last updated on Nov 11 2025 by Munyoki Kilyungi
...mkdir -p /var/guix/profiles/per-user/laminar
chown -R laminar:laminar /var/guix/profiles/per-user/laminar
```
... the CI progressed further but now fails when attempting to build guix-past.
- Make build green
✓ issue opened on Dec 21 2021 by BonfaceKilz, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
.../store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv failed
View build log at '/var/log/guix/drvs/l5/hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv.bz2'.
guix...
- GN3 Setup on tux01 - Non-Deterministic Behavior
✓ issue opened on Jan 15 2024 by Munyoki Kilyungi, last updated on Feb 10 2024 by Munyoki Kilyungi
...steps:
```
source /var/guix/profiles/per-user/aruni/current-guix/etc/profile
guix pull -C channels.scm -p ~/.guix-extra-profiles/genenetwork
. .guix-extra-profiles/genenetwork/etc/profile
guix...
- guix build gn-uploader: error
✓ issue opened on Mar 13 2024 by Frederick Muriuki Muriithi, last updated on Jun 19 2025 by Pjotr Prins
...do ~guix pull~ in case the version of guix I had was the problem to no avail.
I have even attempted checking out
=> https://git.genenetwork.org/guix-bioinformatics/commit/?h=fred-updates-20240313&id...
- GN1 Pairscan
✓ issue opened on Sep 15 2021 by Pjotr Prins, last updated on Dec 17 2022 by Pjotr Prins
...@tux01:~$ ~/opt/guix/bin/guix --version
guix (GNU Guix) 1.2.0-12.dffc918
```
First update guix with
```
gn1@tux01:~$ ~/opt/guix/bin/guix pull -p ~/opt/guix-latest
```
followed by the git repos above.
- genecup is currently running as root on penguin2.
✓ issue opened on Aug 15 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
...like this:
guix system: warning: Consider running 'guix pull' followed by
'guix system reconfigure' to get up-to-date packages and security updates.
guile: warning: failed to install locale
Backtrace...
- Python Requests Error in Container
✓ issue opened on Nov 01 2024 by Frederick Muriuki Muriithi, last updated on Nov 07 2024 by Frederick Muriuki Muriithi
...guix-profile/lib/locale"
See the "Application Setup" section in the manual, for more info.
guix (GNU Guix) 2394a7f5fbf60dd6adc0a870366adb57166b6d8b
Copyright (C) 2024 the Guix authors
License GPLv3+...
- Refresh Token Failure
✓ issue opened on Jan 08 2025 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
.../c4508901027a2d3ea98e1e9b3f8767a455cad02f
=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=955e4ce9370be9811262d7c73fa5398385cc04d8
# Closed as Obsolete
We no longer rely on refresh tokens.
- Set-up Virtuoso+Xapian on Production
✓ issue opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Oct 28 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
...guix shell guile-dbi -m manifest.scm -- \
./generate-ttl-files.scm --settings conn-dev.scm --output \
/export2/guix-containers/genenetwork-development/var/lib/virtuoso \
--documentation /tmp/doc-...
- Migrate to Python3.10
✓ issue opened on Jul 12 2023 by Frederick Muriuki Muriithi, last updated on Oct 11 2023 by Munyoki Kilyungi; 0 of 1 tasks done
...Libraries
* [ ] yoyo-migrations
* others ...
### Migration Notes
This error in guix-forge:
```
bonfacem@tux02 ~ $ zcat /var/log/guix/drvs/d6/48xcspiykyhcink41968zhfr15w2d5-guix-forge.drv.gz
(repl-...
- Genenetwork3 Effective UID
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
...(see `guix/least-authority.scm` in the GNU Guix repository), which is essentially a container within the main container. As such, it is necessary to expose any file paths (via the `#:mappings` keyword)...
- Need Guix packages
✓ issue opened on Mar 12 2022 by Pjotr Prins, last updated on Oct 11 2023 by Munyoki Kilyungi
...Guix packages
This link used to show the guix packages:
=> https://genenetwork.org/environments/
It somehow got reverted and is out of date. Please see if we can get a list again that does not slow...
- Remove externally loaded JS
✓ issue opened on Apr 18 2022 by BonfaceKilz, last updated on Feb 28 2024 by Alexander_Kabui; 3 of 3 tasks done
...CDN. This needs to be packaged and loaded from our GNU Guix profile.
## Tasks
* [x] Package `jquery-ui`.
* [x] Replace `jquery-ui` cdn with a link from the GNU Guix profile.
* [x] Check and report if...
- Update RDF Generation and Ingress to Virtuoso
✓ issue opened on Oct 15 2024 by Munyoki Kilyungi, last updated on Jan 06 2026 by Munyoki Kilyungi
...the recent modified RIF+WIKI models:
```
# Generate the RDF triples
time guix shell guile-dbi guile-hashing -m manifest.scm -- ./pre-inst-env ./examples/generif.scm --settings conf.scm --output /home/...
- 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
..."/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/local/guix-...
- gn-guile: Activations on Production not Running as Expected
✓ issue opened on Aug 15 2025 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi
...guix's `least-authority-wrapper` we can no longer write to the root filesystem ("/"). That is not much of a problem.
So I tried adding `#:directory (dirname gn-doc-git-checkout)` to the `make-forkexec-...
- Virtuoso: Shutdown Clears Data
✓ issue opened on Oct 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 30 2024 by Frederick Muriuki Muriithi
...bulk loading
=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=2dc335ca84ea7f26c6977e6b432f3420b113f0aa Add configs for scheduler and checkpointing
=> https://git.genenetwork.org/guix-...
- gn-uploader container: Running wrong genenetwork2
✓ issue opened on Mar 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...guix, gn-uploader
## Description
I build the uploader container with Genenetwork2, commit b9e04ad, as shown:
```
$ guix gc -R /usr/local/bin/genenetwork-uploader-container | grep genenetwork2
/gnu/...
- Add search syntax hints to web UI
✓ issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...how mumi (the Guix issue tracker) hints at the search query syntax when you click on the "Hint" dropdown.
=> https://issues.guix.gnu.org/
This will serve as a kind of self-documentation. It will keep...
- Profiling GN
✓ issue opened on Jul 23 2025 by Munyoki Kilyungi, last updated on Feb 03 2026 by Munyoki Kilyungi
...can use gprof2dot to visualise the profile
```
guix shell gprof2dot -- gprof2dot -f pstats 1753202013-GET-show_trait-37931ms.prof > 1753202013-GET-show_trait-37931ms.prof.dot
guix shell xdot -- xdot...
- test1-auth.genenetwork.org Can't Find Templates
✓ issue opened on Mar 02 2024 by Frederick Muriuki Muriithi, last updated on Jun 26 2024 by Frederick Muriuki Muriithi
...-02 01:39:53 jinja2.exceptions.TemplateNotFound: admin/login.html
2024-03-02 01:39:53 Exception on /auth/admin/login [GET]
︙
```
Checking the install:
```
$ fredm@tux02:~$ guix gc -R /usr/local/bin/...
- metadata caching bug
✓ issue opened on Mar 18 2022 by Alexander Kabui, last updated on Dec 23 2022 by Pjotr Prins; 2 of 2 tasks done
...recent call last):
File "/usr/local/guix-profiles/gn-latest-20220122/lib/python3.9/site-packages/flask/app.py", line 1513, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/guix-...
- Error when fetching SNPs in a search page
✓ issue opened on Sep 28 2022 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
...call last):
File "/usr/local/guix-profiles/gn-latest-20220122/lib/python3.9/site-packages/flask/app.py", line 1513, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/guix-...
- Better Logging
✓ issue opened on Aug 23 2022 by Munyoki Kilyungi, last updated on Oct 12 2022 by Munyoki Kilyungi
...org/guix-bioinformatics/guix-bioinformatics/commit/e80fe4ddcf15e21004b8135cf8af34b458697f64
Removing the 404's would prevent us from catching important errors if ever they occur. I suggest we fix...
- Phenotype Correlation Error
✓ issue opened on Sep 28 2022 by Zachary Sloan, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
...call last):
File "/usr/local/guix-profiles/gn-latest-20220820/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/guix-...
- Fix possible python 3.10 linting errors after bump from 3.9
✓ issue opened on Jun 06 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...guix upgrade, there were some failing python 3.10 linting and mypy errors:
```
➜ main [guix-dev]: pylint sheepdog/worker.py gn3/ tests
************* Module gn3.db_utils
gn3/db_utils.py:24:8: W2301...
- Remove `bin/genenetwork2` Script
✓ issue opened on Sep 04 2025 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi; 6 of 6 tasks done
...following mandatory environment variables:
* GN2_PROFILE
* GN2_SETTINGS
* JS_GUIX_PATH
* GEMMA_COMMAND
* PLINK_COMMAND
* GEMMA_WRAPPER_COMMAND
* REQUESTS_CA_BUNDLE
Within a guix shell, you could do...
- GEMMA output differs from R/qtl2
✓ issue opened on Aug 01 2024 by Pjotr Prins, last updated on Sep 20 2024 by Pjotr Prins
...is packaged in guix and can be run in a shell with
```
guix shell -C r r-qtl2
> library(qtl2)
> bxd <- read_cross2(file = "bxd_cancer_new_GN_July_2024.json")
Warning messages:
1: In recode_geno(sheet...
- Login issues with gn-auth
✓ issue opened on Mar 01 2024 by Pjotr Prins, last updated on Jul 03 2024 by Frederick Muriuki Muriithi
...genenetwork.org cannot write to the database file.
Possible confirmation of the hypothesis:
The cd container is built with the following options:
```
container_script=$(guix system container --network...
- Upload probeset metadata
✓ issue opened on Jun 19 2023 by Munyoki Kilyungi, last updated on Jun 26 2023 by Munyoki Kilyungi
...dirs
=> https://gitlab.com/genenetwork/guix-bioinformatics/-/merge_requests/24 Add dirs-allowed to virtuoso configs
The public-sparql and genenetwork-development containers were re-built to apply...
- Rework Test: Remove redis as Test Dependency
✓ issue opened on Oct 27 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...deployed, or remove them completely from the system.
### Update 2024-02-27
The system was updated to use prefixed keys, and the full tests now run correctly. Still need to add the tests to the guix CI/...
- Move Uploader to tux02
✓ issue opened on Mar 12 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 3 of 3 tasks done
...-uploader, guix, container, deploy
## Databases
### MariaDB
To avoid corrupting the data on CI/CD, we need to run a separate database server.
This implies separate configurations, and separate startup.
- genenetwork2 CD sometimes fails to restart
✓ issue opened on Mar 17 2023 by Arun Isaac, last updated on Jul 29 2024 by Munyoki Kilyungi
...suspect this is not a problem with the CI/CD Guix configuration, but rather with genenetwork2 itself. More debugging is necessary.
A reminder that CD logs are publicly accessible on tux02.
=> /topics/...
- issues/binderlite/add-spinner-for-submit-form.gmi
✓ issue opened on Nov 10 2021 by jgart, last updated on Dec 22 2021 by Frederick Muriuki Muriithi
...be built? A spinning guix gnu logo could be cool.
https://www.w3schools.com/howto/howto_css_loader.asp
https://spin.js.org/https://spin.js.org/
## Solution
We're using ansi2html now.
See the following...
- Add Documentation For Set Up and Data Retrieval For AI Repo
✓ issue opened on Dec 01 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...the guix documentation for the AI repo.
* Sharing TTL Information and Processing How-To
* Share alternate way of getting sparql json-ld data from public endpoint outside isql.
* Share json-ld gotchas.
- Implementing parallel correlation with rust
✓ issue opened on Apr 25 2022 by Alexander Kabui, last updated on Jul 11 2023 by Alexander_Kabui; 12 of 15 tasks done
...parralel
## Tasks
* [X] implementation of basic pearson and spearman correlation in rust
* [X] add unittests and benchmarks
* [X] loading datasets;format
* [X] package the library as a guix package...
- Configurations
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...reduces the mental overhead of dealing with multiple places to fetch the configs.
From these, the CI/CD system can them build and intern the configurations into the store with guix functions like...
- Handling Resource Links in ProbeSet Page
✓ issue opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Dec 14 2023 by Munyoki Kilyungi
...file get's too big.
### Resolution
Transforming ProbeSet metadata takes long. The exact command:
```shell
time guix shell guile-dbi \
guile-hashing -m manifest.scm \
-- ./pre-inst-env...
- issues/fetch-sample-data.gmi
✓ issue opened on Aug 09 2021 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
...assumes 2 parents and 2 F1s). They're
currently hard-coded in webqtlUtil.py.
[0]
[1] * Tasks, Guix
:ARCHIVE: /home/bonface/Self/org/archive/2021_guix.org_archive::
#### Wed 25 May 2022 21:59:52 EAT...
- uACME Error: "urn:ietf:params:acme:error:unauthorized"
✓ issue opened on Oct 19 2025 by Frederick Muriuki Muriithi, last updated on Oct 20 2025 by Frederick Muriuki Muriithi
...guix container exec 89086 /run/current-system/profile/bin/bash --login
root@sparql /# cd /var/run/acme/acme-challenge/
root@sparql /var/run/acme/acme-challenge# while true; do ls; sleep 0.5; clear...
- Haley-Knott Regression Mapping Error
✓ issue opened on Sep 11 2024 by Frederick Muriuki Muriithi
.../guix-bioinformatics/commit/?id=7a1bf5bc1c3de67f01eabd23e1ddc0150f81b22b
# Footnotes
[fn:1] https://github.com/genenetwork/genenetwork2/blob/50fc0b4bc4106164745afc7e1099bb150f6e635f/gn2/utility/Plot...
- R/qtl JSONDecodeError
✓ issue opened on Dec 23 2022 by Pjotr Prins, last updated on Dec 24 2022 by Pjotr Prins; 3 of 3 tasks done
...a problem with R. Zach says there is a problem with the load path in
=> ./genenetwork3/scripts/rqtl_wrapper.R
The current Guix profile is in
```
export GN2_PROFILE=/home/zas1024/opt/gn-latest-20221206...