GUIX OS with GeneNetwork

COMPUTER

Guix OS install involves downloading the iso; setting it on a flash disk with: dd if=guix.iso of=/dev/sdX status=progress; and using the graphical guide. Some quirks I got were:

I needed an internet connection but wifi didn't work out of the box. I used USB tethering though.
I forgot to edit the final configuration to UEFI. To boot, I used grub by:

# ref: https://superuser.com/a/1512531
set pager=1
ls
# find the drive that has guix_os by searching for /etc/config.scm file
cat drive_from_ls/etc/config.scm # e.g. cat (hd0,1)/etc/config.scm
set root=drive_from_ls # e.g. set root=(hd0,1)
cat /boot/grub/grub.cfg
# run the commands in the menuentry manually
linux /gnu/store/......
initrd /gnu/store/.....
# boot the OS
boot

I changed my bootloader config in /etc/config.scm to fix the efi issue

;; Ref: https://guix.gnu.org/manual/en/html_node/Bootloader-Configuration.html#index-bootloader_002dconfiguration
(bootloader (bootloader-configuration
  (bootloader grub-efi-bootloader)
  (targets '("/boot/efi"))
  (keyboard-layout keyboard-layout)))

and rebuild the OS with sudo guix system reconfigure --allow-downgrades /etc/config.scm - I experienced screen flickering in my terminal and modified my boot parameters to fix it:

;; ref: https://wiki.archlinux.org/title/Intel_graphics#Screen_flickering
(bootloader (bootloader-configuration
              (bootloader grub-efi-bootloader)
              (targets '("/boot/efi"))
              (keyboard-layout keyboard-layout)))
(kernel-arguments (list "i915.enable_psr=0"))

Quality of Life Changes

Zsh as default shell

Change /etc/config.scm to have:

;; ref: https://lists.gnu.org/archive/html/help-guix/2017-07/msg00024.html
;; added this
(use-package-modules shells)

(users (cons* (user-account
                (name "rookie")
                (comment "rookie")
                (group "users")
                (home-directory "/home/rookie")
                ;; added this line
                (shell #~(string-append #$zsh "/bin/zsh))
                (supplementary-groups '("wheel" "netdev" "audio" "vidoe")))
            %base-user-accounts))

When installing oh-my-zsh I also got an error: ZSH not installed and I had to do an extra guix install zsh.

Non Guix

Non Guix Reference

For wifi to work, I modified /etc/config.scm to have:

;; non free linux module
(use-modules (nongnu packages linux)
             (nongnu system linux-initrd))

(operating-system
  (kernel linux)
  (firmware (list linux-firmware))

The README did most of the heavy lifting, but I couldn't figure out how to add the substitutes.

;; what ended up in my services section
  (services
   (append (list (service xfce-desktop-service-type)

                 ;; To configure OpenSSH, pass an 'openssh-configuration'
                 ;; record as a second argument to 'service' below.
                 (service openssh-service-type)
                 (service cups-service-type)
                 (set-xorg-configuration
                  (xorg-configuration (keyboard-layout keyboard-layout))))

           ;; This is the default list of services we
           ;; are appending to.
           ;; %desktop-services)
                (modify-services %desktop-services
                     (guix-service-type config => (guix-configuration
                       (inherit config)
                       (substitute-urls
                        (append (list "https://substitutes.nonguix.org")
                          %default-substitute-urls))
                       (authorized-keys
                        (append (list (plain-file "non-guix.pub"
                                                ;; output from https://substitutes.nonguix.org/signing-key.pub
                                                ;; merged into one line
                                                  "(public-key (ecc (curve Ed25519) (q #C1FD53E5D4CE971933EC50C9F307AE2171A2D3B52C804642A7A35F84F3A4EA98#)))"
                                                  ))

                          %default-authorized-guix-keys))))))
   )

Locale Bug

I couldn't get tmux to start, getting tmux: invalid LC_ALL, LC_CTYPE or LANG and running locale -a failed too. The root cause was that my applications were built on a different version of glibc and running guix update fixed this.

GeneNetwork Setup

Follow the instructions here to set up genenetwork

Small changes:

# pick the channels file from 
curl https://ci.genenetwork.org/channels.scm > channels.scm
# gn2 setup
guix pull -C channels.scm -p ~/.guix-extra-channels/gn2
GUIX_PROFILE=$HOME/.guix-extra-profiles/gn2
. $GUIX_PROFILE/etc/profile
guix install genenetwork2 -p ~/.guix-extra-channels/gn2
guix install genenetwork3 -p ~/.guix-extra-channels/gn2 # setups an older version

# gn3 setup
guix pull -C channels.scm -p ~/.guix-extra-channels/gn3
GUIX_PROFILE=$HOME/.guix-extra-profiles/gn3
. $GUIX_PROFILE/etc/profile
guix install genenetwork3 -p ~/.guix-extra-channels/gn3
guix install genenetwork2 -p ~/.guix-extra-channels/gn3
guix package -i python-mysqlclient -p ~/.guix-extra-channels/gn3
guix package -i python-pyld -p ~/.guix-extra-channels/gn3
pytest -k unit_tests # succeeds after this
pytest # still fails
FLASK_DEBUG=1 FLASK_APP="main.py" flask run --port=8080 # works

# gn-auth set up is a bit different from the above
# the README is clear in this case
# just make sure you have genenetwork2 and genetwork3 installed in the profile