- Guix installation and versions
document created on Jan 24 2026 by Pjotr Prins, last updated on Jan 24 2026 by Pjotr Prins
guix -V
guix (GNU Guix) 1.4.0
Copyright (C) 2022 the Guix authors
```
to really see the exact version, use
```
guix describe
guix a259069
repository URL: https://git.guix.gnu.org/guix.git...
- Guix packages
document created on Dec 23 2022 by Pjotr Prins, last updated on Dec 21 2025 by Pjotr Prins
...Codeberg):
```
guix pull -p ~/opt/guix-pull --url=https://codeberg.org/guix/guix
```
Now Guix should be happy with
```
~/opt/guix-pull/bin/guix package -L ~/guix-bioinformatics/ -L ~/guix-past/modules/...
- Set up Guix for new users
document created on Oct 17 2024 by Arun Isaac, last updated on Oct 17 2024 by Arun Isaac
...guix pull
"Borrow" some other user's guix to run guix pull. In the example below, we use root's guix, but it might as well be any guix.
```
$ /var/guix/profiles/per-user/root/current-guix/bin/guix...
- Installation with Guix
document created on Jun 18 2023 by Pjotr Prins, last updated 3 weeks ago by Pjotr Prins
...Guix website.
=> https://guix.gnu.org/en/download/
and run (as root)
```
sh guix-install.sh
```
Debian-derived distros (no longer) may support
```
apt-get install guix
```
# Update Guix with our guix-...
- Building Guix packages for RISC-V
document created on Apr 08 2022 by Arun Isaac
...guix-bioinformatics channel
The guix-bioinformatics channel provides statically linked versions of smithwaterman and wfmash.
=> https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics guix-...
- Updating Guix profiles (for production and development)
document created on Jun 14 2022 by Arun Isaac, last updated on Jan 24 2026 by Pjotr Prins
...like
```
tux01:~$ ~/opt/guix-pull/bin/guix pull -C channels.scm -p ~/opt/guix-gn-channel
tux01:~$ ~/opt/guix-gn-channel/bin/guix package -i genenetwork2 -p /usr/local/guix-profiles/gn-latest-yyyymmdd...
- Attaining Build Sanity
document created 8 weeks ago by Munyoki Kilyungi, last updated 7 weeks ago by Munyoki Kilyungi
.../guix-science/guix-past guix-past: Old software that is no longer available in mainline GNU Guix that we still depend on.
=> https://codeberg.org/guix/guix-rust-past-crates.git guix-rust-past-crates...
- 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...
- 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...
- 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...
- Guix Rust Bootstrap
document created on Oct 22 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
...version of Guix. This is achieved with 'guix pull' and making sure it works.
```sh
mkdir -p ~/opt
guix pull -p ~/opt/guix-pull --url=https://codeberg.org/guix/guix
```
it takes a few minutes. Next set...
- 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...
- Writing a guix package with Claude code
document created 3 weeks ago by Pjotr Prins, last updated 3 days ago by Pjotr Prins
...$HOME/.claude --share=$HOME/tmp=/tmp --expose=$HOME/iwrk/opensource/guix/guix-master/gnu=$HOME/guix-gnu --expose=$HOME/iwrk/opensource/guix/contrib/=$HOME/guix-contrib --share=/var/guix/daemon-socket/...
- 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/...
- Fixating Guix for GN
document created on Dec 21 2025 by Pjotr Prins
...Guix! That version is defined here:
=> https://git.genenetwork.org/gn-machines/tree/.guix-channel
Note that guix-forge and guix-bioinformatics are *also* fixated. The idea is that we only upgrade GN...
- 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.
- Guix system containers and how we use them
document created on Mar 31 2023 by Arun Isaac, last updated 3 days ago by Pjotr Prins
...use Guix system containers. Note that Guix system containers are different from guix shell containers (and the older guix environment containers). guix shell containers are meant for interactive use...
- Binding notebooks
document created on Aug 22 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...guix.info/blog/2019/10/towards-reproducible-jupyter-notebooks/ Guix Jupyter Magics
## Misc Binder Lite Ideas
Should binder-lite be a distribution of GNU Guix System?
GeneNetwork can provide custom ISO...
- Update production checklist
document created on May 10 2025 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins
.../guix/guix -p ~/opt/guix-pull
```
Use that also to install guix in /usr/local/guix-profiles
```
guix package -i guix -p /usr/local/guix-profiles/guix
```
and update the daemon in systemd accordingly.
- Make build green
✓ issue opened on Dec 21 2021 by BonfaceKilz, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
.../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 build...
- Building a ~guix pack~ for Environment Sharing
document created on Sep 13 2022 by Frederick Muriuki Muriithi, last updated on Dec 03 2023 by Pjotr Prins
...demonstration
> guix pack -RR -S /mybin=bin -S /mylib=lib \
> -L /home/frederick/genenetwork/guix-bioinformatics \
> python redis mariadb genenetwork-qc
* The `-RR` option ensures `guix pack`...
- Starting GN1
document created on Dec 08 2022 by Pjotr Prins, last updated on Jun 13 2025 by Pjotr Prins
...Guix container.
Start a screen and run the guix deploy script. See the README file in
gn1@tux01:~/production/gnshare/gn
# Guix
At this point GN1 is fixed at Feb 2021:
guix: 1.2.0-12.dffc918
guix-past...
- GN Services
document created on Sep 15 2021 by Pjotr Prins, last updated on Dec 23 2022 by Pjotr Prins
...gn3
alias guix=~/opt/guix/bin/guix
gn3@tux01:~/production/gn-proxy
source .guix-deploy
raco pkg install --auto
env TMPDIR=/home/gn3/tmp SQL_USER=*** SQL_PASSWORD=*** racket -L info server/rest.rkt...
- Deploying genecup
document created on Apr 22 2025 by Pjotr Prins, last updated 118 minutes ago by Pjotr Prins
...profile which includes guix-bioinformatics, using genecup-channels.scm.
# shepherd@tux02:~/services/genecup$ ./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/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-...
- R
document created on Feb 10 2024 by Pjotr Prins, last updated on Feb 12 2024 by Pjotr Prins
...guix you get newer packages(!). We typically handle guix through a profile with
```
guix pull -p ~/opt/guix
~/opt/guix/bin/guix --version
```
So, use the latter if you want to be up-to-date. A '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...
- Debugging and developing code
document created on Mar 19 2024 by Pjotr Prins, last updated on Aug 20 2025 by Pjotr Prins
...guix-bioinformatics from `.config/guix/channels.scm` and now do a guix pull using the local repo:
```
guix pull -p ~/opt/guix-dev
```
To get a channel list from an existing guix try `guix describe -f...
- PubMed local
document created 3 weeks ago by Pjotr Prins
...-pubmed -https -step DAT
guix shell -L ../guix-bioinformatics -L . edirect-25 coreutils -- env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source archive-pubmed -https -step DWN
guix shell -L ../guix-...
- IMPG AGC bindings
document created on Oct 22 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
...guix pull and set it up in a profile
```sh
guix pull -p ~/opt/guix-pull --url=https://codeberg.org/guix/guix
```
it takes a few minutes. Next set the environment
```sh
unset GUIX_PROFILE
. ~/opt/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
...INFO
### 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-...
- Running postgres in a Guix container
document created on Jan 17 2023 by Pjotr Prins
...guix (note the leading dot)
```
. ~/opt/guix-pull/etc/profile
```
Install postgres (here we opt for v14) with
```
guix packages -A postgres
mkdir -p ~/data/pgdata
cd ~/data
guix shell -C -N postgresql@...
- 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...
- 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-...
- Fallbacks
document created on Feb 18 2024 by Pjotr Prins, last updated on Apr 09 2024 by Pjotr Prins
...guix
* [X] Make sure guix is on a large partition (200Gb)
* [X] Update guix in /usr/local/guix-profiles
* [X] Disable default guix on Debian
* [X] Reboot
* [X] Update nftables
Having issues with sdd...
- 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...
- GeneNetwork Releases
document created on Feb 10 2025 by Frederick Muriuki Muriithi
...(openpgp-fingerprint
"7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3"))))
(channel
(name 'guix-past)
(url "https://gitlab.inria.fr/guix-hpc/guix-past")...
- 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...
- 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
...carried over to the shell script, but it seems not
* Had to run 'guix pull' to update the guix tree for genecup, since the guix-bioinformatics repository had made breaking changes since the last time.
- Fire up system container for GN
document created on Mar 02 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins
...systemreboot.net/guix-forge/
branch: main
commit: 6c622a67051c22eeefe37eedb17d427fbb70c99b
guix-past 921f845
repository URL: https://gitlab.inria.fr/guix-hpc/guix-past
branch: master...
- Deploy GeneNetwork
document created on Jan 18 2023 by Arun Isaac, last updated on Aug 27 2024 by Frederick Muriuki Muriithi
...deploying, guix, guix container, guix system container
* status: in progress
# Description
This page attempts to document the deployment process we have for GeneNetwork. We use Guix system containers...
- 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...
- Weechat
document created on Nov 04 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Guix. Current install using a guix environment:
```
env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/opt/guix-latest/bin/guix environment --ad-hoc coreutils weechat weechat-matrix weechat-wee-slack nss-...
- Shepherd
document created on Aug 27 2021 by Pjotr Prins, last updated on Dec 02 2023 by Pjotr Prins
...daemon
Wants=guix-daemon.service
[Service]
Type=simple
ExecStart=/var/guix/profiles/per-user/shepherd/guix-profile/bin/shepherd
User=shepherd
Group=shepherd
LimitNOFILE=8000
[Install]
WantedBy=multi-...
- GNSoC 2023
document created on Jun 21 2023 by Pjotr Prins, last updated on Aug 24 2023 by Pjotr Prins
...progress
### Week 1
* Proposal written
- guix pull on guix-bioinformatics
- updated guix is broken gemma (Pjotr)
* Efraim guix GN2 - so we can have a channel
* Next step build substitutes for 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...
- topics/xapian/xapian-indexing-on-tux01.gmi
document created on Jul 27 2023 by Zachary Sloan, last updated on Dec 03 2023 by Pjotr Prins
...guix shell:
/home/zas1024/opt/guix/bin/guix shell --container --network --share=/export/data/genenetwork/ --development --file=guix.scm
Run the indexer script:
env PYTHONPATH=. python3 scripts/index-...
- Modifying dump macros
document created on Jul 01 2023 by Munyoki Kilyungi
.../guix/nonguix/signing-key.pub")
(local-file "/etc/guix/guix-past/signing-key.pub"))
%default-authorized-guix-keys)))))
```
The above snippet demonstrates how you can modify...
- 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+...
- Implementation of storing genotypes in LMDB
issue opened 2 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...
- Running pudb From an External Environment
document created on Dec 03 2023 by Pjotr Prins
...pip install pudb
3) Run the GN3 container, exposing the new virtual environment with something like:
* env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ~/.config/guix/current/bin/guix...
- Fire up system container for GN-QA System
document created on May 13 2024 by Munyoki Kilyungi, last updated on May 13 2024 by Munyoki Kilyungi
...using the latest gn-auth code. The one in guix-bioinformatics is stale.
There was an error when displaying the error page. Fixed upstream in guix-bioinformatics:
=> https://git.genenetwork.org/guix-...
- Cosigt (on Octopus)
document created 3 weeks ago by Pjotr Prins
...Guix packages so we can migrate and upgrade much easier.
# Guix
cosigt requires the following packages. Already in guix are:
* bedtools 2.31
* bioconductor-rtracklayer=1.62.0
* htslib=1.22
* kfilt...
- CI/CD for genetwork projects
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Jul 22 2025 by Pjotr Prins
...GN3
Arun has figured out the CI part. It runs a suitably configured laminar CI service in a Guix container created with `guix system container'.
=> https://git.systemreboot.net/guix-forge/about/...
- Configuring Nginx on the Host System
document created on Aug 27 2024 by Frederick Muriuki Muriithi
...deploying, nginx, guix, guix container, guix system container
* status: in progress
## Introduction
We deploy the GeneNetwork system within GNU Guix system containers. All the configurations...
- Moving /gnu
document created on Apr 13 2024 by Pjotr Prins, last updated on Apr 13 2024 by Pjotr Prins
...guix on the tuxes and, oops:
> Sat, Apr 13, 2024, 11:54:32 - pjotrp:
```
root@tux06:/home/wrk# ls -l /export/octopus01/guix-profiles/slurm-1-link/sbin/munged
ls: cannot access '/export/octopus01/guix-...
- 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.
- Deploying gn-auth
document created on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Mar 12 2024 by Frederick Muriuki Muriithi
...pull origin main
```
4. Now get a guix shell:
```
$ ~/opt/guix/bin/guix shell --container --network --share=../auth-run-migrations.db=/home/fredm/auth-run-migrations.db --development --file=guix.scm...
- 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
...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
* [x]...
- 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...
- Jupyter notebooks
document created on Sep 01 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Guix
Jupyter notebooks can be installed in a profile
```
~/opt/guix-latest/bin/guix package -i jupyter python-pandas vim screen tree -p ~/opt/jupyter
source ~/opt/jupyter/etc/profile
jupyter notebook...
- Developer links for
document created on May 06 2022 by Arun Isaac, last updated on Oct 16 2022 by Pjotr Prins
...org/fredmanglis/gnqc_py Quality control
=> https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics guix-bioinformatics Guix channel
=> https://git.genenetwork.org/arunisaac/dump-...
- CI Rethink slides
document created on Jul 13 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
...slides
## Background
* guix-forge is an independent general purpose project that powers our CI
* guix-forge is built on laminar
* CI jobs are just simple scripts
* scripts are written in G-expressions...
- Install and use Claude Code using Guix
document created 8 weeks ago by Pjotr Prins, last updated 7 weeks ago by Johannes Medagbe
...dependency.
The shell prompt looks like:
```
mkdir workdir && cd workdir
mkdir -p $HOME/.local $HOME/.cache/claude $HOME/.claude
guix shell -C -N -F curl bash openssl nss-certs coreutils grep sed jq...
- Virtuoso
document created on Aug 27 2021 by Pjotr Prins, last updated on Aug 20 2025 by Pjotr Prins
...guix-bioinformatics channel. The easiest way to run virtuoso is to use the virtuoso service to run it in a guix system container. The only downside of this method is that, since guix system containers...
- Generating Key-Pairs
document created on Apr 18 2024 by Frederick Muriuki Muriithi, last updated on Apr 22 2024 by Frederick Muriuki Muriithi
...client.
## Exposing the Key-Pairs to Guix shell/container
The generated keys above do not need to be modified within the running application, so we will use the "--expose" option e.g.
```
$ guix...
- 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-...
- 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...
- Slurm User Guide on Octopus HPC
document created on Feb 11 2024 by Pjotr Prins, last updated 118 minutes ago by Pjotr Prins
...the modern Guix packaging system. In the future we may add Nix support too.
An example of using R with guix is described here:
=> ../../hpc/guix/R
If you choose, you can still use conda, brew, spack...
- Setting up Local Development Database
document created on Aug 19 2022 by Frederick Muriuki Muriithi, last updated on Aug 01 2024 by Arun Isaac
...1 (Using Guix system containers)
Setting up mariadb in a Guix container is the preferred and easier method. But, you need root access to run the container. The genenetwork2 repo comes with a guix...
- Octopussy needs love
document created on Dec 21 2025 by Pjotr Prins, last updated on Feb 10 2026 by Pjotr Prins
...-toolchain
autoreconf -f -i
make
```
Next I created a guix package that installs with:
```
guix build -L ~/guix-bioinformatics -L ~/guix-past/modules moosefs
```
See
=> https://git.genenetwork.org/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-...
- 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-...
- OpenSMTPD
document created on May 27 2023 by Pjotr Prins
Guix comes with a default opensmtp service, so let's try and get that running as a system container for reasons of deployment. See also
=> ../deployment.gmi
Setting up a mail service with Guix...
- Using autossh to Keep SSH Tunnels Alive
document created on Apr 23 2025 by Alexander_Kabui, last updated on May 14 2025 by Frederick Muriuki Muriithi
...tunnel, alive
## TL;DR
```
guix package -i autossh # Install autossh with Guix
autossh -M 0 -o "ServerAliveInterval 60" -o "ServerAliveCountMax 5" -L 4000:127.0.0.1:3306 alexander@remoteserver.org...
- [gn3/ADR-002] Move RDF Test Cases to Build Container
document created on Sep 30 2024 by Munyoki Kilyungi, last updated on Oct 02 2024 by Munyoki Kilyungi
...in the ".guix/genenetwork3-all-tests.scm" file instead of the main "genenetwork3" package definition in guix-bioinformatics. This way, we have all our "light" tests I.e. unit tests running in guix-...
- BNW interface for GN2
document created on Oct 18 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...guix environment --ad-hoc php -- php-fpm --fpm-config php-fpm.conf
# Launch nginx
guix environment -L guix-past/modules -L guix-bioinformatics bnw --ad-hoc nginx -- nginx -p...
- Utility Scripts
document created on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Dec 03 2023 by Pjotr Prins
...guix shell --container --network --share=/export/data/genenetwork-sqlite \
--development --file=guix.scm
[env] $ python3 -m scripts.register_sys_admin \
/export/data/genenetwork-sqlite/auth...
- 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-...
- Octopus Maintenance
document created on Feb 13 2023 by Pjotr Prins, last updated on Jan 17 2026 by Pjotr Prins
...-0.5.13 (2017-09-26)
sbatch --version
slurm-wlm 18.08.5-2
```
To install 'munge', go to 'octopus01' and run:
```shell
guix package -i munge@0.5.14 -p /export/octopus01/guix-profiles/slurm
systemctl...
- Genenetwork3 Effective UID
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
...Wrapper (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`...
- 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...
- R/qtl2
document created on Oct 07 2024 by Pjotr Prins
...cross (CC). It also comes with an LMM implementation. Here we describe using and embedding R/qtl2 in GN2.
# Tasks
## R/qtl2
R/qtl2 is packaged in guix and can be run in a shell with
```
guix shell -C...
- Setting Up a Basic Pre-Commit Hook for Linting Scheme Files
document created on Aug 07 2024 by Munyoki Kilyungi, last updated on Aug 07 2024 by Munyoki Kilyungi
.../hooks/pre-commit
#!/bin/sh
# Run guix style on staged .scm files
for file in $(git diff --cached --name-only --diff-filter=ACM | grep ".scm$"); do
if ! guix style --whole-file "$file"; then
echo...
- Mechanical Rob
document created on Aug 23 2022 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
...Mechanical Rob locally by following the steps below:
(note that these steps are mostly the same ones to run GN2 locally).
1. Get a guix shell for GN2 development:
```
$ cd genenetwork2/
$ guix shell...
- 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
...`jquery-ui` is still loaded from a 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...
- Guides Vs References
document created on Jul 16 2024 by John Nduli, last updated on Jul 17 2024 by John Nduli
...actionable steps.
* Avoid stream of consciousness writing.
### Example
Wrong:
When setting up guix OS, I couldn't get `tmux` to start, getting `tmux: invalid LC_ALL, LC_CTYPE or LANG`. Running `locale...
- 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/...
- Working with Virtuoso for Local Development
document created on Sep 20 2024 by Munyoki Kilyungi, last updated on Sep 20 2024 by Munyoki Kilyungi
...guix, install the Virtuoso server:
```
guix install virtuoso-ose # or any other means to install virtuoso
cd /path/to/virtuoso/database/folder
cp $HOME/.guix-profile/var/lib/virtuoso/db/virtuoso.ini...
- UTHSC VPN with free software
document created on Aug 22 2022 by Arun Isaac, last updated on Jul 05 2025 by Pjotr Prins
...guix. See below. It should just work, provided you have the chained certificate that you can get from the browser or one of us and point to the right server. Simply
```
$(guix build -f uthsc-vpn.scm)...
- 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-...
- 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-...
- 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...
- R/qtl2 LMDB Adapter
document created on Sep 04 2025 by Alexander_Kabui, last updated on Oct 20 2025 by Frederick Muriuki Muriithi
...currently supported formats are JSON and YAML.
Example:
```sh
guix shell python-click python-lmdb python-wrapper python-pyyaml -- \
python dump_metadata.py dump-cross [LMDB_PATH] [CROSS_FILE_PATH]...
- 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...
- 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-...
- Precompute mapping input data
document created on Apr 23 2025 by Pjotr Prins, last updated on Jul 29 2025 by Pjotr Prins
...Debian Guix images!
git clone https://git.genenetwork.org/guix-bioinformatics/
git clone https://gitlab.inria.fr/guix-hpc/guix-past
~/opt/guix-pull/bin/guix package -L ~/guix-bioinformatics/ -L ~/guix-...
- 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...
- Moosefs
document created on Jan 01 2026 by Pjotr Prins, last updated on Feb 10 2026 by Pjotr Prins
.../usr/local/guix-profiles/moosefs/sbin/mfsmaster -d start -c /etc/mfs/mfsmaster.cfg -x
ExecStop=/usr/local/guix-profiles/moosefs/sbin/mfsmaster -c /etc/mfs/mfsmaster.cfg stop
ExecStop=/usr/local/guix-...
- 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-...
- 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-...
- 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...
- 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
...syntax. For example, see 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-...
- Profiling GN
✓ issue opened on Jul 23 2025 by Munyoki Kilyungi, last updated on Feb 03 2026 by Munyoki Kilyungi
...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 1753202013-GET-...
- Singularity on Octopus
document created 3 weeks ago by Pjotr Prins, last updated 3 days ago by Pjotr Prins
...727 possibilities? (y or n)
Singularity vsoch-hello-world-master-latest.simg:~> cat /etc/issue
Ubuntu 14.04.6 LTS \n \l
```
# Create singularity image from guix package
```
guix pack -f squashfs -S...
- Running snakemake workflows on octopus
document created on Feb 12 2026 by Arun Isaac
First, drop into a guix shell with snakemake and the slurm plugin.
```
guix shell snakemake python python-snakemake-executor-plugin-slurm python-snakemake-executor-plugin-slurm-jobstep
```
Assuming...
- Octopus pages/links
document created 3 weeks ago by Pjotr Prins
...pages/links
=> ../hpc/octopus/slurm-user-guide Slurm user guide
=> set-up-guix-for-new-users Guix for new users
=> recent-rust Running a recent rust
=> running-snakemake-workflows Running snakemake...
- Useful Shell Scripts
document created on Oct 06 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...-within-dir /tmp"
* Choose a guix profile on the fly: ",choose-profile":
```
#!/bin/env sh
# To run this use source!
GUIX_PROFILE="$(guix package --list-profiles | fzf --multi)"
export GUIX_PROFILE
.
- Migrate GN1 Clustering
document created on Jul 18 2021 by Pjotr Prins, last updated on Mar 22 2022 by Frederick Muriuki Muriithi
.../guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm
frederick@galadriel-ubuntu ~/genenetwork/genenetwork3 [env]$ python3
Python 3.8.2 (default, Jan 1 1970...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
..."/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-profiles/gn-...
- Our virtuoso instances
document created on Mar 31 2023 by Arun Isaac, last updated on Aug 20 2025 by Pjotr Prins
...Guix configuration file to find the correct port. But, here is a summary for quick lookup. Please fix this if it is inaccurate.
### Internal production virtuoso on tux01
* Server port: 8891
* SPARQL...
- 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-...
- Lisp For Schemers
document created on Dec 29 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...-FROM NIL
(SB-LOOP::LOOP-COLLECT-ANSWER #:LOOP-LIST-HEAD-493))))))
T
```
#### Using iota from the alexandria library with GNU/Guix:
```
guix shell sbcl sbcl-alexandria rlwrap -- rlwrap sbcl...
- How to upgrade slurm on octopus
document created on Aug 29 2024 by Arun Isaac, last updated on Oct 18 2024 by Arun Isaac
...slurmd
```
Upgrade slurm, passing slurm-worker-deploy.sh the slurm store path obtained from building slurm using guix build on octopus01. Recall that you cannot invoke guix build on the worker nodes.
- Use a recent Rust on Octopus
document created on Jun 04 2025 by Pjotr Prins
...in Debian
or Guix. No panic, because Rust has few requirements.
Install latest rust using the script
```
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
```
Set path
```
. ~/.cargo/env...
- Meeting Notes
document created on Jun 11 2024 by John Nduli, last updated on Jan 10 2025 by Munyoki Kilyungi
Guix Root Container
- With docker, to prevent the need for sudo, we usually create a docker group, and add users that need to run this to this group. Can this ahppen in guix?
- Guix has a guix...
- Logging with Flask and Gunicorn
document created on Apr 15 2024 by Frederick Muriuki Muriithi
...palletsprojects.com/en/3.0.x/ 3. Flask Web-Application Framework
=> https://gunicorn.org/ 4. Green Unicorn (gunicorn) WSGI Server
=> https://guix.gnu.org/ 5. GNU Guix
=> https://trstringer.com/logging-...
- Orchestration and fallbacks
document created on Sep 02 2022 by Pjotr Prins, last updated on Oct 25 2022 by Pjotr Prins
.../shiny power service Dave
* [ ] biohackrxiv
* [ ] hegp
* [ ] covid19
* [ ] guix publish server (runs on penguin2, needs tux02 @efraimf)
I am still missing a few! All run by a man and his diligent dog.
- 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...
- 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
...(template)
2024-03-02 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...
- 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
...I'm currently 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...
- 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-...
- 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...
- 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 the...
- 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-...
- Genotype database
document created on Jun 03 2022 by Arun Isaac, last updated on Apr 27 2024 by Pjotr Prins
...attentive reader familiar with Guix might note the similarities between the layout of the genodb database and that of Guix's /gnu/store. Indeed, both genodb and the Guix store are functional databases.
- 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...
- Precompute PublishData
document created on Oct 29 2025 by Pjotr Prins, last updated on Dec 19 2025 by Pjotr Prins
...guix from
guix describe Thu Mar 14 21:33:55 2024
to
guix describe Sun Aug 10 18:18:20 2025
Should use a newer version first! Let's try
```
guix pull --url=https://codeberg.org/guix/guix -p ~/opt/guix-...
- 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
...guile 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...
- Debug RISC-V assembly with QEMU and GDB
document created on Oct 19 2022 by Arun Isaac
...-V assembly code, run it in the QEMU emulator and debug it using GDB, the GNU debugger.
First, we write a short manifest file so that we can pull in all the tools we need using the ever-convenient Guix.
- Lizard maintenance
document created on Jul 18 2021 by Pjotr Prins, last updated on Jan 11 2026 by Pjotr Prins
.../local/guix-profiles/octo/sbin/mfschunkserver -c /etc/lizardfs/mfschunkserver_hdd.cfg -d start
ExecReload=/bin/kill -HUP $MAINPID
Restart=on-abort
OOMScoreAdjust=-999
IOAccounting=true
IOWeight=250...
- Login issues with gn-auth
✓ issue opened on Mar 01 2024 by Pjotr Prins, last updated on Jul 03 2024 by Frederick Muriuki Muriithi
...genenetwork.org cannot write to the database file.
Possible confirmation of the hypothesis:
The cd container is built with the following options:
```
container_script=$(guix system container --network...
- 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.
- 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 the...
- Prevent Weak Passwords
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
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 definition...
- 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
...CD. I 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.
- 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...
- 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.
- Octopus HPC
document created on Feb 10 2024 by Pjotr Prins
Octopus HPC
We run the Octopus HPC service described on
=> https://genenetwork.org/facilities
Here we aggregate some common topics.
=> ../../topics/hpc/guix/R Running R
- Hoot Genome Browser
document created on Sep 23 2025 by Pjotr Prins, last updated on Sep 24 2025 by Johannes Medagbe
...mapping
# Tasks
* [ ] Embed hoot browser in GN2 as a pilot
* + [ ] Guix package for JS and minimal JBrowse2?
* + [ ] Embedding code in GN2
* [ ] Create two tracks for QTL comparisons - vector...
- Julia Deployment
document created on Apr 01 2024 by Pjotr Prins
...Deployment
GN deploys Julia, first for a pluto notebook container and second for computing linear mixed models (LMM).
h
=> https://github.com/sens/FaSTLMM.jl
# Tasks
* [ ] Compile FaSTLMM using a Guix...
- Continuous Deployment logs
document created on Feb 15 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
...continuously deployed development instances of genenetwork may be found at /export2/guix-containers/genenetwork-development/var/log/cd in tux02.
This documentation may be out of date. So, if you can't...
- Aider
document created on Oct 29 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
Aider
=> https://aider.chat/
```
apt-get install python3-venv # or use guix
python3 -m venv ~/opt/python-aider
~/opt/python-aider/bin/python3 -m pip install aider-install
export PATH="/home/wrk/...
- Security
document created on Sep 09 2025 by Pjotr Prins
...guix system containers (a kind of light weight Docker setup).
# ssh
Secure shell is very important. First we disable password logins. We use keys only. We also limit AllowUsers because it is flexible...
- Pangenotypes
document created on Oct 11 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
...AA
NODE 5 GeneE allele=AG
# Edges section: EDGE <from_id> <to_id>
EDGE 1 2
EDGE 1 3
EDGE 2 4
EDGE 3 4
EDGE 4 5
EDGE 5 1
```
the tooling
=> https://github.com/aprilweilab/grgl.git
builds with
```
guix...
- 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...
- MariaDB
document created on May 10 2025 by Pjotr Prins, last updated on May 14 2025 by Frederick Muriuki Muriithi
...-guix.service. Restore the latest backup archive and overwrite the existing database directory at /var/lib/mysql. Finally, restart the service. Note that /var/lib/mysql is actually a symbolic link to...
- 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
...generated 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-...
- 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
...'/tmp/gn2/83f0831af5911ab6dc62cbbd37d13741.csv'
```
So, GN2 is miscommunicating the path to GN3.
This also led to documenting how one should test GN2 and GN3 in a running VM:
=> /topics/guix/guix-...
- 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...
- 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...
- Test pangenome derived genotypes
document created on Nov 04 2025 by Pjotr Prins, last updated on Jan 17 2026 by Pjotr Prins
...load it with isql (note it may be worth search-replacing the gnt:run tag to something descriptive).
```
cd /export/guix-containers/virtuoso/data/virtuoso/ttl/
guix shell -C -N --expose=/export/guix-...
- Large Language Models (LLMs) & Metadata
document created on Jun 23 2023 by Solomon Shelby, last updated on Jan 12 2024 by Solomon Shelby
...guix package for flask site
* [X] 5 - Serve GNQA on tux02
* [-] 5.5 - Get feedback from testers of GNQA
* [ ] 6 - Improve GNQA after evaluating feedback
* [ ] 6.5 - Add reference rating to GNQA
* [X]...
- 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
.../scripts/rqtl_wrapper.R
The current Guix profile is in
```
export GN2_PROFILE=/home/zas1024/opt/gn-latest-20221206
```
So we can run a shell
```
source /home/zas1024/opt/gn-latest-20221206/etc/profile...
- Stand-up Notes
document created on Oct 04 2025 by Munyoki Kilyungi
...forge/guix-bioinformatics upgrades that affect prod
* Support work for GNQA: sane gn-qna(fahamu)/AI deploys; Review Johannes' work; Help with tuning models; play catch up (cover up knowledge gap)...
- 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...
- GeneNetwork Hacking Documentation
document created on Mar 11 2022 by Frederick Muriuki Muriithi, last updated on Jul 18 2022 by Frederick Muriuki Muriithi
...datasets, hacking
## Unifying Principles
Like GNU Guix has the concepts of Packages, Monads, G-Expressions and the like as some of the unifying principles that help with understanding, contributing...
- Installing GPU on Balg01 server
document created on Oct 04 2025 by Pjotr Prins, last updated on Oct 07 2025 by Pjotr Prins
...Using Guix python I ran:
```
pip install "gpu-benchmark-tool[nvidia]"
```
of course it downloads a ridiculous amount of binaries... But then we can run
```
export PATH=/home/wrk/.local/bin:$PATH
gpu-...
- 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
...guix version of mariadb in /usr/local/guix-profiles (don't use Debian!!)
* [X] repair borg backup
* [X] Stop old mariadb (on new host tux02)
* [X] backup old mariadb database
* [X] restore 'sane'...
- Editing Data
document created on Nov 23 2021 by BonfaceKilz, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
...app.run(host='0.0.0.0',
port=SERVER_PORT,
debug=True,
```
- As a work-around for the failing gn2 build, install pudb in it's own profile
```
guix install pudb -p ~/opt/...
- Developing against GeneNetwork
document created on Jun 18 2023 by Pjotr Prins, last updated on Dec 03 2023 by Pjotr Prins
...//localhost:8080" \
GN3_LOCAL_URL="http://localhost:8081 "\
./etc/default_settings.py -c \
../test/requests/test-website.py -a http://localhost:5003
```
The GN2_PROFILE is the Guix profile...
- 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...
- Backup Drops
document created on Sep 22 2025 by Pjotr Prins, last updated on Sep 24 2025 by Johannes Medagbe
...permitted
```
This means you need to set the suid on the fusermount3 command. Bit nasty in Guix.
```
apt-get install fuse(3) sshfs
chmod 4755 /usr/bin/fusermount
```
If auth.log says error: /dev/pts/...
- Borg backups
document created on Feb 09 2025 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins
...guix. This should really be done as the borg user (ibackup).
```
ibackup@tux03:~$ mkdir ~/opt
ibackup@tux03:~$ guix package -i borg -p ~/opt/borg
~/opt/borg/bin/borg --version
1.2.2
```
# Create a...