[ENH][systoleos] First commit

.gitmodules

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+[submodule "guix-systole-artwork"]
+	path = guix-systole-artwork
+	url = [email protected]:SystoleOS/guix-systole-artwork.git

README.md

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+# SystoleOS Guix definition
+
+This is a definition for SystoleOS, a 3D Slicer-centric operating system based on GNU Guix that provides a modularised version of 3D Slicer and comes preconfigured with the `guix-systole` Guix channel.
+
+## Cloning the repository
+
+This repository contains a git submodule. In order to clone it locally, run `git clone --recurse-submodules https://github.com/OUH-MESHLab/BrainlabMirror`. If you have already cloned the repository without the `--recurse-submodules` flag, run the following from within the repository: `git submodule update --init`.
+
+## Generating a SystoleOS image
+
+Guix needs to be setup on the system in order to use this definition.
+
+For the time being, this definition needs the `guix-systole` repository to be cloned locally. Clone it with the command `git clone https://github.com/SystoleOS/guix-systole --branch dev` in a local path.
+
+The image can then be generated by `cd`ing to this repository and executing the command `guix system image -L path/to/guix-systole/repo -t iso9660 systoleos/brainlabmirror.scm`. Guix will then provide the path to the generated image in the Store.
+
+The `brainlabmirror` image provides a full image with adjustments meant to run on bare metal. If you only need an image for a VM, then replace `brainlabmirror.scm` with `base.scm`.
+
+N.B.: to build the `brainlabmirror` image, the building machine needs to be configured to pull from the Nonguix channel. See how [here](https://gitlab.com/nonguix/nonguix/-/blob/master/README.org?ref_type=heads&plain=1#L43).
+
+Other types of images can also be generated. For example, to generate an image to run with QEMU/KVM, use `-t qcow2`, then boot into the generated virtual disk with QEMU.
+
+To find out which image types are available, run `guix system image --list-image-types`.
+
+## Generating a VM
+
+Guix can generate a VM out of an OS definition and provide a script to run the VM.
+
+This feature depends on QEMU/KVM.
+
+To do so, run `guix system vm systoleos/base.scm`. Guix will then provide the path to a Bash script in the Store.
+
+This script can be run with arguments to pass directly to QEMU. For example, to enable networking and request 1GB of RAM (from the [Guix manual](https://guix.gnu.org/manual/en/html_node/Invoking-guix-system.html#index-virtual-machine)):
+
+`/gnu/store/…-run-vm.sh -m 1024 -smp 2 -nic user,model=virtio-net-pci`
+
+Refer to the [Guix manual](https://guix.gnu.org/manual/en/html_node/Invoking-guix-system.html) for more details.

systoleos/base.scm

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+;; This operating-system image definition can be built with:
+;; `guix system image -L . -t iso9660 systoleos/base.scm`
+
+(define-module (systoleos base)
+  #:use-module (guix channels)
+  #:use-module (guix gexp)
+  #:use-module (guix build utils)
+  #:use-module (guix build-system trivial)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages vim)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages mtools)
+  #:use-module (gnu packages package-management)
+  #:use-module (gnu packages terminals)
+  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages conky)
+  #:use-module (gnu packages image-viewers)
+  #:use-module (gnu packages fonts)
+  #:use-module (gnu packages wm)
+  #:use-module (gnu packages kde-frameworks)
+  #:use-module (gnu packages xfce)
+  #:use-module (gnu services)
+  #:use-module (gnu services base)
+  #:use-module (gnu services guix)
+  #:use-module (gnu services desktop)
+  #:use-module (gnu services xorg)
+  #:use-module (gnu services lightdm)
+  #:use-module (gnu services networking)
+  #:use-module (gnu system)
+  #:use-module (gnu system image)
+  #:use-module (gnu system install)
+  #:use-module (gnu system shadow)
+  #:use-module (gnu system file-systems)
+  #:use-module (gnu system keyboard)
+  #:use-module (gnu system setuid)
+  #:use-module (gnu bootloader)
+  #:use-module (gnu bootloader grub)
+  #:use-module (gnu image)
+  #:use-module (gnu packages)
+  #:use-module (gnu home)
+  #:use-module (gnu home services)
+  #:use-module (guix-systole services dicomd-service)
+  #:use-module (guix-systole packages slicer)
+  #:use-module (guix-systole packages openigtlink))
+
+;; https://substitutes.nonguix.org/signing-key.pub
+(define %signing-key
+  (plain-file "nonguix.pub"
+   "(public-key
+ (ecc
+  (curve Ed25519)
+  (q #C1FD53E5D4CE971933EC50C9F307AE2171A2D3B52C804642A7A35F84F3A4EA98#)))"))
+
+(define %channels
+  (cons* (channel
+           (name 'guix-systole)
+           (url "https://github.com/SystoleOS/guix-systole")
+           (branch "dev")
+         %default-channels))
+
+(define serialise-channels
+  (scheme-file "channels.scm"
+               #~(begin
+                   (with-output-to-file %output
+                     (lambda ()
+                       (display (sexp->string '%
+                                              (%channels)))
+                       (newline))))))
+
+;; Fluxbox configuration inspired by guix-psy-dicom
+;; https://github.com/OUH-MESHLab/guix-psy-dicom/blob/enhancement/psydicom_system/config.scm
+(define conkyrc
+  (local-file "etc/conky/conky.conf"))
+(define fluxbox-init
+  (local-file "etc/fluxbox/init"))
+(define fluxbox-keys
+  (local-file "etc/fluxbox/keys"))
+(define fluxbox-startup
+  (local-file "etc/fluxbox/startup"))
+(define ideskrc
+  (local-file "etc/idesk/ideskrc"))
+(define idesk-icon-lnk
+  (local-file "etc/idesk/DICOMStore.lnk"))
+(define nftables-config
+  (local-file "etc/misc/nftables.conf"))
+(define user-home
+  (home-environment
+    (packages (list slicer-5.8 slicer-openigtlink))
+    (services
+     (cons* (service home-xdg-configuration-files-service-type
+                     `())
+            (service home-files-service-type
+                     `((".fluxbox/init" ,fluxbox-init)
+                       (".fluxbox/keys" ,fluxbox-keys)
+                       (".fluxbox/startup" ,fluxbox-startup)
+                       (".idesktop/DICOMStore.lnk" ,idesk-icon-lnk)
+                       (".conkyrc" ,conkyrc)
+                       (".ideskrc" ,ideskrc))) %base-home-services))))
+
+(define-shepherd-service-type slicer-autostart-type
+  (start (lambda* (#:key outputs #:allow-other-keys)
+           (let* ((slicer-bin
+                   (string-append (assoc-ref outputs "out") "/Slicer-wrapper"))
+                  (uid (user-uid "brainlabmirror")))
+             ;; shepherd/execute runs as root by default; this drops to the user
+             ; (invoke "su" "-l" "brainlabmirror" "-c" slicer-bin))))
+             (invoke "exec" slicer-bin)
+  (stop  (lambda args
+           (shepherd-send :TERM "Slicer")))
+  (description "Autostart 3D Slicer at login"))
+
+(define systoleos-base
+  (operating-system
+    ; (inherit installation-os)
+
+    (host-name "systole")
+    (timezone "Europe/Oslo")
+
+    ;; Use the UEFI variant of GRUB with the EFI System
+    ;; Partition mounted on /boot/efi.
+    (bootloader (bootloader-configuration
+                  (bootloader grub-efi-bootloader)
+                  (targets '("/boot/efi"))))
+
+    ;; Assume the target root file system is labelled "root",
+    ;; and the EFI System Partition has UUID 1234-ABCD.
+    (file-systems (append (list (file-system
+                                  (device (file-system-label "root"))
+                                  (mount-point "/")
+                                  (type "ext4"))
+                                (file-system
+                                  (device (uuid "1234-ABCD"
+                                                'fat))
+                                  (mount-point "/boot/efi")
+                                  (type "vfat"))) %base-file-systems))
+
+    ;; The `brainlabmirror` account must be initialised with `passwd` command
+    (users (append (list (user-account
+                           (name "brainlabmirror")
+                           (comment "BrainLab")
+                           (password "")
+                           (group "users")
+                           (supplementary-groups (list "dicom" "netdev"
+                                                       "audio" "video")))
+                         (user-account
+                           (name "admin")
+                           (comment "Admin")
+                           (group "users")
+                           (supplementary-groups (list "wheel" "netdev"
+                                                       "audio" "video" "wheel"))))
+                   %base-user-accounts))
+
+    (sudoers-file (plain-file "sudoers"
+                              (string-append (plain-file-content
+                                              %sudoers-specification)
+                                             (format #f
+                                              "~a ALL = NOPASSWD: ALL~%"
+                                              "admin"))))
+
+    (setuid-programs (append (list (setuid-program
+                                   (program (file-append sudo "/bin/sudo"))))
+                           %setuid-programs))
+
+    (packages (append (list
+                       ;; Slicer
+                       ; slicer-5.8
+
+                       ;; terminal emulator
+                       xterm
+
+                       ;; utils
+                       git
+                       curl
+                       vim
+
+                       ;; desktop environment
+                       conky
+                       feh
+                       fluxbox
+                       font-bitstream-vera
+                       font-dejavu
+                       idesk
+                       oxygen-icons
+                       thunar) %base-packages))
+
+    (services
+     (append (list
+
+                   ;; LightDM display manager
+                   ;; Configuration documentation: https://guix.gnu.org/manual/en/html_node/X-Window.html
+                   (service lightdm-service-type
+                            (lightdm-configuration (allow-empty-passwords? #t)
+                                                   (debug? #t)
+                                                   (xdmcp? #t)
+                                                   (vnc-server? #f)
+                                                   (greeters (list (lightdm-gtk-greeter-configuration
+                                                                    (allow-debugging?
+                                                                     #t))))
+                                                   (seats (list (lightdm-seat-configuration
+                                                                 (name "*")
+                                                                 (autologin-user
+                                                                  "brainlabmirror")
+                                                                 (user-session
+                                                                  ;; "xfce.desktop"
+                                                                  "fluxbox"))))))
+
+                   ;; Services for xfce desktop environment
+                   ;; (service xfce-desktop-service-type)
+
+                   ;; nftables service
+                   (service nftables-service-type
+                            (nftables-configuration (ruleset (local-file
+                                                              "etc/nftables.conf"))))
+
+                   (service guix-home-service-type
+                            `(("brainlabmirror" ,user-home)))
+
+                   (set-xorg-configuration
+                    (xorg-configuration (keyboard-layout (keyboard-layout
+                                                          "altgr-intl")))
+                    lightdm-service-type)
+
+                   ;; Use Dicomd service defined in guix-systole
+                   (service dicomd-service-type)
+
+                   ;; Include the channel file so that it can be used during installation
+                   (extra-special-file "/etc/guix/channels.scm"
+                                       serialise-channels)
+
+                   ;; Symlink background artwork into the OS image
+                   (extra-special-file
+                     "/run/current-system/profile/share/backgrounds/systole/Systole_Magnet_base_1280_1024.png"
+                     (local-file "../guix-systole-artwork/backgrounds/Systole_Magnet_base_1280_1024.png"))
+
+                   ;; Autostart Slicer
+                   (service slicer-autostart-type #t)
+
+                   )
+
+             (modify-services %desktop-services
+               (delete gdm-service-type)
+               (guix-service-type config =>
+                                  (guix-configuration (inherit config)
+                                                      (guix (guix-for-channels
+                                                             %channels))
+                                                      (authorized-keys (cons*
+                                                                        %signing-key
+                                                                        %default-authorized-guix-keys))
+                                                      (substitute-urls `(,@%default-substitute-urls
+                                                                         "https://substitutes.nonguix.org"))
+                                                      (channels %channels))))))))
+
+systoleos-base