- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 3 weeks ago by Pjotr Prins; 34 of 74 tasks done
/usr/local/guix-profiles/guix-pull/etc/profile
guix system container --network -L . -L ../guix-forge/guix/ -L ../guix-bioinformatics/ -L ../guix-past/modules/ --substitute-urls='https://ci.guix.gnu...
- CI rethink
issue opened on Jun 23 2023 by Arun Isaac, last updated on Jan 03 2024 by Arun Isaac; 7 of 8 tasks done
...-guix/
* [x] Make genenetwork2 repo a Guix channel
* [x] Make genenetwork3 repo a Guix channel
## Set up CI jobs
We need a CI job to run on every commit to guix-bioinformatics and check if guix pull...
- 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
...by hand by Pjotr)
* hrdp-project (uses shared (broken!) guix profile) (upstream source is gone)
* ratspub (uses own guix profile, uses shared guix-bioinformatics)(deprecated(?))
* pluto (uses own guix...
- guix-bioinformatics: Remove `guix-rust-past-crates` channel
issue opened on Oct 27 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
...guix-bioinformatics, guix-rust-past-crates, guix, rust, crates
## Description
GNU Guix recently changed[1] the way it handles packaging of rust packages.
The old rust packages got moved to the "guix-...
- Cannot Connect to MariaDB
issue opened on Nov 05 2024 by Frederick Muriuki Muriithi, last updated on Nov 08 2024 by Frederick Muriuki Muriithi
...guix "2394a7f5fbf60dd6adc0a870366adb57166b6d8b" into a profile locally: went through without a hitch
Upgrade guix daemon, and restart it. Delete profile and run `guix gc`, then try pulling guix...
- 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
...Setting up Guix
We tend to install software in a guix profile. E.g.
```
guix pull -p ~/opt/guix-pull
. /home/wrk/opt/guix-pull/etc/profile
guix package -i mariadb -p /usr/local/guix-profiles/...
- GN1 metadata
issue opened on Dec 09 2022 by Pjotr Prins; 0 of 3 tasks done
...-apache2-with-php5-and-mysql-support-on-fedora-18-lamp Some hints here.
### Building genenetwork1
For the python2.4 packages
```
gaeta:~/guix-past$ guix build -L ~/guix-past/modules/ -L ~/guix-...
- Deploying GeneNetwork CD
issue opened on Jul 18 2025 by Munyoki Kilyungi, last updated on Jul 18 2025 by Munyoki Kilyungi
...guix pull -C channels.scm -p ~/.guix-extra-profiles/gn-machines --allow-downgrades
guix pull -C channels.scm -p ~/.guix-extra-profiles/gn-machines-shepherd-upgrade --allow-downgrades
```
## Step 2...
- When binderlite finds an unkown package in a guix manifest
issue opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...a guix manifest
What do we do if binderlite finds a package that is not in upstream guix in a
manifest?
This is what it currently does:
```
guix environment: error: guile-pipe: unknown package
guix...
- Guix: Using guix shell with root file
issue opened on Jan 27 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Guix: Using guix shell with root file
## Tags
* assigned: jgart
* type: unclear
* status: unclear
* priority: low
* keywords: guix, guix shell, root file
## Description
```
guix shell --root...
- Implementation of storing genotypes in LMDB
issue opened 3 weeks ago by Alexander_Kabui, last updated 3 days ago by Alexander_Kabui; 8 of 12 tasks done
...Guix installed.
## Quick Start
### 1. Launch Guix Shell with Dependencies
```
guix shell python-wrapper python-click python-lmdb python-numpy python-pytest
```
### 2. Container (Isolated)
```
guix...
- Planned Guix Updates
issue opened on Nov 14 2025 by Munyoki Kilyungi
...guix-bioinformatics, guix
* interested: pjotrp, aruni
## Description
The following outlines issues around the next upgrade:
* Update pinned guix commit to the latest and see whether inferior profiles...
- Migrate Genenetwork Production from tux03 to tux04, Jan2026-Feb2026
issue opened on Jan 21 2026 by Frederick Muriuki Muriithi, last updated on Feb 03 2026 by Frederick Muriuki Muriithi; 8 of 8 tasks done
...Check versions: tux03 has 10.11.11, tux04 has 11.8.3
* [x] What version on guix? I can get 10.11.14
* [x] Look into requirements for running mariadb from guix. Compare to Debian...
- 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
...guix-bioinformatics in 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...
- issues/systems/t02-crash.gmi
issue opened on Aug 12 2025 by Pjotr Prins
...(guix), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
Aug 7 18:16:00 tux02 kernel: [13520227.160945] oom_reaper: reaped process 128091 (guix), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
```
Guix...
- Troubleshooting inside the GN dev container
issue opened on Jul 22 2025 by Munyoki Kilyungi, last updated on Jul 22 2025 by Munyoki Kilyungi
...correct pid and guix/bash path.
sudo /home/bonfacem/.config/guix/current/bin/guix container exec 16182 /gnu/store/m6c5hgqg569mbcjjbp8l8m7q82ascpdl-bash-5.1.16/bin/bash --init-file /home/bonfacem/.guix-...
- Production on tux04
issue opened on May 10 2025 by Pjotr Prins, last updated on May 14 2025 by Frederick Muriuki Muriithi; 10 of 12 tasks done
...3.6T 1.8T 1.7T 52% /export2
```
# Guix
Getting guix going is a bit tricky because we want to keep the store!
```
cp -vau /mnt/old-root/var/guix/ /var/
cp -vau /mnt/old-root/usr/local/guix-...
- 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
...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 /home/gn1/guix-...
- Generate Heatmaps Failing
issue opened on Oct 15 2024 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
...but since guix-bioinformatics pins the guix version to `b0b988c41c9e0e591274495a1b2d6f27fcdae15a`, we are not able to pull in newer versions of packages from guix.
### Update 2025-04-08T10:59CDT
Got...
- 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
...guix guix-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...
- ProbeSetData
issue opened on Dec 31 2021 by Pjotr Prins, last updated on Mar 13 2023 by Pjotr Prins; 15 of 17 tasks done
.../export4/local/home/mariadb$ ~/opt/guix-pull/bin/guix pull -p ~/opt/guix-latest
. ~/opt/guix-latest/etc/profile
mkdir var
guix shell -C -N coreutils sed mariadb --share=var=/var
mysqld_safe --datadir...
- Dumping Probesets from MariaDB to LMDB
issue opened 4 weeks ago by Alexander_Kabui
...Guix environment with Python and dependencies
* Access to GeneNetwork MariaDB database
## Guix Environment Setup
Run with all dependencies:
```
guix shell python-wrapper python-mysqlclient python-...
- Second production on tux02
issue opened on Aug 23 2022 by Arun Isaac, last updated on Sep 05 2022 by Alexander_Kabui
...aruni
Set up a second production system on tux02. This will be fully configured using Guix and will be able to roll back to previous states easily. The Guix configuration of this system should go...
- 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
...com/11820306/82554452-9f53d280-9b6e-11ea-9f17-074f5091de4d.png Screen Shot 2020-05-20 at 10 03 29 PM
### Questions
* What version of datatables or associated extensions is being used in guix?
* Does...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...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 "/usr/local/guix-...
- 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
..."/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 "/usr/local/guix-...
- Tasks
issue opened on Jun 27 2023 by GregFa, last updated on Apr 26 2024 by Pjotr Prins; 0 of 2 tasks done
...guix-shell. E.g.
```
guix shell -C -N --share=$HOME/.julia nss-certs openssl julia julia-csv julia-dataframes julia-datastructures
```
```
julia> using Pkg; Pkg.add("Optim")
Updating registry at...
- 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
...instrumenting the requests. See what hogs up time. Loading the landing page takes up 32 seconds!
Something's off. From outside the container:
```
123bonfacem@tux02 ~ $ guix shell python-wrapper...
- Broken Aliases
issue opened on Oct 21 2024 by Frederick Muriuki Muriithi, last updated on Aug 15 2025 by Frederick Muriuki Muriithi; 3 of 4 tasks done
...Racket - and we don't have much support in Guix. I wrote the code the days after my bike accident:
=> https://github.com/genenetwork/gn3/blob/master/gn3/web/wikidata.rkt
and it is probably easiest to...
- Large datasets crash gemma
issue opened on Mar 12 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 7 tasks done
...Guix:
```
tux02:~/tmp/gemma-cpu-lockup$ /usr/bin/time -v gemma -loco 1 -gk -g HSNIH-Palmer_true_geno.txt -p PHENO_2+FcfQiTVSC7FmmbsatUPg.txt -a HSNIH-Palmer_true_snps.txt
GEMMA 0.98.5-pre1 (2021-08-14)...
- MGAMMA design philosophy
issue opened on Apr 17 2024 by Pjotr Prins, last updated on Oct 27 2024 by Pjotr Prins
...interface proved problematic - and Zig went out of favour because of its bootstrap story which prevents it becoming part of Guix, Debian etc. Also I discovered new tensor MPUs support f64 - so we may...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...in GNU Guix for root scripts
* [ ] list current state - it means parsing the state list (some exists)
* [ ] synchronize between queues using a dump
* [ ] sheepdog_expect.rb - expect PINGs...
- Public inbox
issue opened on Jun 29 2022 by Arun Isaac
...a public inbox based mailing list for genenetwork. Among other things, this could be used to review patches via the email based git workflow. Preferably, set up this public inbox as part of guix-forge.
- Prevent Weak Passwords
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
...passwords.
## Notes
### 2025-12-31: Look Into Libraries
=> https://pypi.org/project/password-strength/ password-strength
The library above seems promising. Unfortunately, we'd have to write a guix...
- Terminal output to the browser
issue opened on Oct 28 2021 by jgart, last updated on Oct 07 2022 by Arun Isaac
...SourceHut suite. builds.sr.ht generates terminal output using jinja templates and a relatively small python library called ansi2html. It is already packaged by guix upstream as python-ansi2html (It...
- 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
...running VM:
=> /topics/guix/guix-system-containers-and-how-we-use-them.gmi
and fixing the shared TMPDIR. The next step however fails with
```
sh: line 1: Rscript: command not found
2024-04-01 07:33:13...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...good news is that these tools are in the GUIX profile already.
=> Commit aa4048af0f633101f2e723d86b5e99590885f2df fixes the network graph
Still, the PDF is empty. ps2pdf is used - but I think the ps...
- Speeding up GEMMA
issue opened on Nov 11 2025 by Pjotr Prins, last updated on Dec 12 2025 by Pjotr Prins; 5 of 15 tasks done
...arch optimizations (even though Cooperlake suggests differently). Another potential optimization is to use a fast malloc library. We do, however, already compile with a recent gcc, thanks to Guix. No...
- Benchmark DuckDB against LMDB for storing genotypes
issue opened 3 days ago by Alexander_Kabui
...LMDB → DataFrame merge
* [ ] measure ingestion pipeline end-to-end time
* [ ] document Guix shell environment (duckdb python package + pyarrow)
* [ ] write ADR if DuckDB proves beneficial
## Open...
- Tux04/Tux05 disk issues
issue opened on May 03 2024 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins; 12 of 12 tasks done
...3
innodb_purge_threads=0
```
Make sure to disable (and restart) once it is up and running!
So the steps are:
* [X] install updated guix version of mariadb in /usr/local/guix-profiles (don't use Debian...
- Multivariate GEMMA hangs (issue 243)
issue opened on Aug 16 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...GNU Guix:
Profiling above gemma dataset
```
120 7.3% 7.3% 155 9.4% CalcQi
96 5.8% 13.1% 96 5.8% dgemm_kernel_ZEN
88 5.3% 18.4% 88 5.3% __sched_yield...
- Prompt As UI
issue opened on Feb 18 2026 by Munyoki Kilyungi, last updated 2 weeks ago by Munyoki Kilyungi; 40 of 43 tasks done
...to guix-bioinformatics. Questions: langchain support? Cancelled. Poor guix support for AI libraries. We work with pip+pyproject for now.
## Build search corpus wth phenotype metadata
* Naive...