diff options
Diffstat (limited to 'gn/services')
| -rw-r--r-- | gn/services/ratspub-container.scm | 129 |
1 files changed, 0 insertions, 129 deletions
diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm deleted file mode 100644 index 1bf9fc6..0000000 --- a/gn/services/ratspub-container.scm +++ /dev/null @@ -1,129 +0,0 @@ -(define-module (gn services ratspub-container)) - -(use-modules (gnu) - (gn packages ratspub) - (guix download) - (guix modules) - (guix packages) - (guix records) - (ice-9 match)) -(use-service-modules shepherd) -(use-package-modules certs compression) - -(define-record-type* <ratspub-configuration> - ratspub-configuration - make-ratspub-configuration - ratspub-configuration? - (package ratspub-configuration-package ; package - (default ratspub))) - -(define %punkt.zip - (origin - (method url-fetch) - (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip") - (sha256 - (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s")))) - -(define ratspub-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 #$(file-append package "/userspub.sqlite") data_dir) - (chmod (string-append data_dir "/userspub.sqlite") #o554)))))))) - -(define ratspub-shepherd-service - (match-lambda - (($ <ratspub-configuration> package) - (with-imported-modules (source-module-closure - '((gnu build shepherd) - (gnu system file-systems))) - (list (shepherd-service - (provision '(ratspub)) - (requirement '(networking)) - (modules '((gnu build shepherd) - (gnu system file-systems))) - (start #~(make-forkexec-constructor/container - (list #$(file-append package "/server.py")) - ;; Needs to run from the directory it is located in. - #:directory #$package - #:log-file "/var/log/ratspub.log" - ;; We don't need to set TMPDIR because we're inside a container. - #:environment-variables - '("EDIRECT_PUBMED_MASTER=/export2/PubMed" - "NLTK_DATA=/var/cache/nltk_data" - "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt") - #:mappings (list (file-system-mapping - (source "/export2/PubMed") - (target source) - (writable? #t)) - (file-system-mapping - (source "/export/ratspub") - (target source) - (writable? #t)) - (file-system-mapping - (source "/var/cache/nltk_data") - (target source)) - (file-system-mapping - (source "/etc/ssl/certs") - (target source))))) - (stop #~(make-kill-destructor)))))))) - -(define ratspub-service-type - (service-type - (name 'ratspub) - (extensions - (list - (service-extension shepherd-root-service-type - ratspub-shepherd-service) - (service-extension activation-service-type - ratspub-activation) - ;; Make sure we get all the dependencies of RatsPub. - (service-extension profile-service-type - (compose list ratspub-configuration-package)))) - (default-value (ratspub-configuration)) - (description - "Run a RatsPub Webserver."))) - -(operating-system - (host-name "ratspub") - (timezone "Etc/UTC") - (locale "en_US.utf8") - - (bootloader (bootloader-configuration - (bootloader grub-bootloader) - (targets '("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)) - - (services (list (service ratspub-service-type - (ratspub-configuration - ;; ratspub for docker, ratspub-with-tensorflow-native for architecture specific speed optimizations. - ;(package ratspub)))))) - (package ratspub-with-tensorflow-native)))))) - -;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/ratspub-container.scm --network --share=/export2/PubMed=/export2/PubMed --share=/export/ratspub=/export/ratspub -;; 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/ratspub-container.scm --network -;; Docker instructions: -;; docker load --input ratspub-docker-image.tar.gz -;; docker run -d --privileged --net=host --name ratspub --volume /path/to/PubMed:/export2/PubMed guix |