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Diffstat (limited to 'gn/services/genecup-container.scm')
| -rw-r--r-- | gn/services/genecup-container.scm | 129 |
1 files changed, 129 insertions, 0 deletions
diff --git a/gn/services/genecup-container.scm b/gn/services/genecup-container.scm new file mode 100644 index 0000000..eae3f9c --- /dev/null +++ b/gn/services/genecup-container.scm @@ -0,0 +1,129 @@ +(define-module (gn services genecup-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* <genecup-configuration> + genecup-configuration + make-genecup-configuration + genecup-configuration? + (package genecup-configuration-package ; package + (default genecup))) + +(define %punkt.zip + (origin + (method url-fetch) + (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip") + (sha256 + (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s")))) + +(define genecup-activation + (match-lambda + (($ <genecup-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 #$(file-append package "/userspub.sqlite") data_dir) + (chmod (string-append data_dir "/userspub.sqlite") #o554)))))))) + +(define genecup-shepherd-service + (match-lambda + (($ <genecup-configuration> package) + (with-imported-modules (source-module-closure + '((gnu build shepherd) + (gnu system file-systems))) + (list (shepherd-service + (provision '(genecup)) + (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/genecup.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 genecup-service-type + (service-type + (name 'genecup) + (extensions + (list + (service-extension shepherd-root-service-type + genecup-shepherd-service) + (service-extension activation-service-type + genecup-activation) + ;; Make sure we get all the dependencies of RatsPub. + (service-extension profile-service-type + (compose list genecup-configuration-package)))) + (default-value (genecup-configuration)) + (description + "Run a GeneCup Webserver."))) + +(operating-system + (host-name "genecup") + (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 (cons nss-certs %base-packages)) ;(list nss-certs)) + + (services (list (service genecup-service-type + (genecup-configuration + ;; genecup for docker, genecup-with-tensorflow-native for architecture specific speed optimizations. + ;(package genecup)))))) + (package genecup-with-tensorflow-native)))))) + +;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-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/genecup-container.scm --network +;; Docker instructions: +;; docker load --input genecup-docker-image.tar.gz +;; docker run -d --privileged --net=host --name genecup --volume /path/to/PubMed:/export2/PubMed guix |