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(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
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