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