- 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...
- 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...
- Writing a guix package with Claude code
document created 3 weeks ago by Pjotr Prins, last updated 5 days ago by Pjotr Prins
.../guix/guix-master/gnu=$HOME/guix-gnu --expose=$HOME/iwrk/opensource/guix/contrib/=$HOME/guix-contrib --share=/var/guix/daemon-socket/ --expose=/gnu/store
```
This allows us to mount source code dirs...
- 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 system containers and how we use them
document created on Mar 31 2023 by Arun Isaac, last updated 5 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 pull
```
guix pull --url=https://codeberg.org/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...
- 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 2 days ago by Pjotr Prins
...version for the genecup guix profile which includes guix-bioinformatics, using genecup-channels.scm.
# shepherd@tux02:~/services/genecup$ ./guix/bin/guix build -L ~/services/genecup/guix-past/modules...
- 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...
- 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
...from factory/GeneCup):
```
guix shell -L ../guix-bioinformatics -L . edirect-25 coreutils -- env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source archive-pubmed -https -step DAT
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-...
- 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@...
- 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...
- 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")...
- 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...
- 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
...guix-bioinformatics
=> ../../issues/gnsoc-ci-rethink Tracking progress
### Week 1
* Proposal written
- guix pull on guix-bioinformatics
- updated guix is broken gemma (Pjotr)
* Efraim guix GN2...
- 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...
- 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
...deploy, deployment, deploying, nginx, guix, guix container, guix system container
* status: in progress
## Introduction
We deploy the GeneNetwork system within GNU Guix system containers. All...
- 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-...
- 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...
- 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
CI Rethink 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-...
- Install and use Claude Code using Guix
document created 9 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...
- Slurm User Guide on Octopus HPC
document created on Feb 11 2024 by Pjotr Prins, last updated 2 days 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-...
- OpenSMTPD
document created on May 27 2023 by Pjotr Prins
...reasons of deployment. See also
=> ../deployment.gmi
Setting up a mail service with Guix is described in
=> https://guix.gnu.org/en/manual/devel/en/html_node/Mail-Services.html
A service is defined...
- 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...
- 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...
- 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...
- 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...
- 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)...
- 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]...
- 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-...
- 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-...
- Singularity on Octopus
document created 3 weeks ago by Pjotr Prins, last updated 5 days ago by Pjotr Prins
...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 /bin=bin pangenomes bash-minimal --tune...
- 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...
- 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...
- 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
systemctl stop 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...
- 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.
- 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.
- 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-...
- 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...
- 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...
- MariaDB
document created on May 10 2025 by Pjotr Prins, last updated on May 14 2025 by Frederick Muriuki Muriithi
...backup archives.
```
ibackup@penguin2:/export/backup/tux01$ /home/wrk/opt/borg/bin/borg list borg-tux01/
```
Stop the running mariadb-guix.service. Restore the latest backup archive and overwrite the...
- Test pangenome derived genotypes
document created on Nov 04 2025 by Pjotr Prins, last updated on Jan 17 2026 by Pjotr Prins
...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-containers/...
- 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]...
- 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)...
- 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:$PATH
gpu-...
- Editing Data
document created on Nov 23 2021 by BonfaceKilz, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
...app.run(host='0.0.0.0',
port=SERVER_PORT,
debug=True,
```
- As a work-around for the failing gn2 build, install pudb in it's own profile
```
guix install pudb -p ~/opt/...
- Developing against GeneNetwork
document created on Jun 18 2023 by Pjotr Prins, last updated on Dec 03 2023 by Pjotr Prins
...//localhost:8080" \
GN3_LOCAL_URL="http://localhost:8081 "\
./etc/default_settings.py -c \
../test/requests/test-website.py -a http://localhost:5003
```
The GN2_PROFILE is the Guix profile...
- Backup Drops
document created on Sep 22 2025 by Pjotr Prins, last updated on Sep 24 2025 by Johannes Medagbe
...permitted
```
This means you need to set the suid on the fusermount3 command. Bit nasty in Guix.
```
apt-get install fuse(3) sshfs
chmod 4755 /usr/bin/fusermount
```
If auth.log says error: /dev/pts/...
- Borg backups
document created on Feb 09 2025 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins
...guix. This should really be done as the borg user (ibackup).
```
ibackup@tux03:~$ mkdir ~/opt
ibackup@tux03:~$ guix package -i borg -p ~/opt/borg
~/opt/borg/bin/borg --version
1.2.2
```
# Create a...