diff options
Diffstat (limited to 'gn/services')
| -rw-r--r-- | gn/services/pluto.scm | 134 |
1 files changed, 134 insertions, 0 deletions
diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm new file mode 100644 index 0000000..3df804c --- /dev/null +++ b/gn/services/pluto.scm @@ -0,0 +1,134 @@ +(define-module (gn services pluto)) + +(use-modules (gnu) + (gn packages julia) + (guix modules) + (guix records) + (ice-9 match)) +(use-service-modules shepherd) +(use-package-modules + admin + certs) + +(define-record-type* <pluto-configuration> + pluto-configuration + make-pluto-configuration + pluto-configuration? + (package pluto-configuration-package ; package + (default julia-visuals)) + (port pluto-configuration-port ; integer + (default 80))) + +(define %julia-account + (list (user-group + (name "julia") + ;(system? #t) + ) + (user-account + (name "julia") + (group "julia") + ;(system? #t) + (comment "Julia User") + (home-directory "/home/jovyan") + ;(shell (file-append shadow "/sbin/nologin")) + ))) + +;(define pluto-activation +; (match-lambda +; (($ <ratspub-configuration> package) +; #~(begin +; (let ((nltk_data "/var/cache/nltk_data/tokenizers") +; (data_dir "/export/ratspub")) +; (unless (file-exists? "/export2/PubMed") +; (mkdir-p "/export2/PubMed")) +; (unless (file-exists? nltk_data) +; (begin +; ;; The correct way would be to use python-nltk to download the data +; ;; python3 -m nltk.downloader -d /var/cache/nltk_data punkt +; (mkdir-p nltk_data) +; (chdir nltk_data) +; (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip))) +; (unless (file-exists? (string-append data_dir "/userspub.sqlite")) +; (begin +; (install-file #$(file-append package "/userspub.sqlite") data_dir) +; (chmod (string-append data_dir "/userspub.sqlite") #o554)))))))) + +(define pluto-shepherd-service + (match-lambda + (($ <pluto-configuration> package port) + (with-imported-modules (source-module-closure + '((gnu build shepherd) + (gnu system file-systems))) + (list (shepherd-service + (provision '(pluto)) + (requirement '(networking)) + (modules '((gnu build shepherd) + (gnu system file-systems))) + (start #~(make-forkexec-constructor/container + (list #$(file-append package "/runpluto.sh") #$port) + ;; Needs to run from the directory it is located in. + ;#:directory #$package + #:log-file "/var/log/pluto.log" + ;; We don't need to set TMPDIR because we're inside a container. + #:user "julia" + #:group "julia" + #:environment-variables + '(;"JULIA_PROJECT=/home/jovyan" + ;"JULIA_LOAD_PATH=/run/current-system/profile/share/julia/packages/" + ) + #:mappings (list (file-system-mapping + (source "/home/jovyan") + (target source) + (writable? #t)) + ) + )) + (stop #~(make-kill-destructor)))))))) + +(define pluto-service-type + (service-type + (name 'pluto) + (extensions + (list + (service-extension shepherd-root-service-type + pluto-shepherd-service) + ;(service-extension activation-service-type + ; ratspub-activation) + (service-extension account-service-type + (const %julia-account)) + ;; Make sure we get all the dependencies of julia-visuals. + (service-extension profile-service-type + (compose list pluto-configuration-package)))) + (default-value (pluto-configuration)) + (description + "Run a Pluto Jupyter Webserver."))) + +(operating-system + (host-name "pluto") + (timezone "Etc/UTC") + (locale "en_US.utf8") + + (bootloader (bootloader-configuration + (bootloader grub-bootloader) + (target "does-not-matter"))) + (file-systems (list (file-system + (device "does-not-matter") + (mount-point "/") + (type "does-not-matter")))) + ;; TODO: A more minimal kernel for use in a docker image + ;; (kernel linux-libre-vm) + ;; No firmware for VMs. + (firmware '()) + (packages ;(list nss-certs) + %base-packages + ) + + (services (list (service pluto-service-type + (pluto-configuration + (port "4343")))))) + +;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/pluto.scm --network +;; For docker it isn't necessary to list the shared folders at build time. +;; guix system docker-image -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/pluto.scm --network +;; Docker instructions: +;; docker load --input pluto-docker-image.tar.gz +;; docker run -d --privileged --net=host --name pluto guix |