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| -rw-r--r-- | gn/services/bh20-seq-resource-container.scm | 106 |
1 files changed, 106 insertions, 0 deletions
diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm new file mode 100644 index 0000000..0114625 --- /dev/null +++ b/gn/services/bh20-seq-resource-container.scm @@ -0,0 +1,106 @@ +(define-module (gn services bh20-seq-resource-container)) + +(use-modules (gnu) + (gn packages bioinformatics) + (guix modules) + ((guix packages) #:select (package-source)) + (guix records) + (ice-9 match)) +(use-service-modules shepherd) +(use-package-modules compression python python-web) + +(define-record-type* <covid19-pubseq-configuration> + covid19-pubseq-configuration + make-covid19-pubseq-configuration + covid19-pubseq-configuration? + (package covid19-pubseq-configuration-package ; package + (default bh20-seq-resource)) + (deploy-directory covid19-pubseq-deploy-directory ; string + (default "/srv/http")) + (port covid19-pubseq-configuration-port ; string + (default "5000"))) + +(define covid19-pubseq-activation-service + (match-lambda + (($ <covid19-pubseq-configuration> package deploy-directory port) + #~(begin + (let ((pkg-src #$(package-source package))) + (when (file-exists? #$deploy-directory) + (delete-file-recursively (mkdir-p #$deploy-directory))) + (mkdir-p #$deploy-directory) + (if (file-is-directory? pkg-src) + (copy-recursively pkg-src #$deploy-directory) + (begin + (copy-file pkg-src #$(string-append deploy-directory + "/src.tar.xz")) + (with-directory-excursion #$deploy-directory + (invoke #$(file-append xz "/bin/xz") "-d" "src.tar.xz") + (invoke #$(file-append tar "/bin/tar") "xvf" "src.tar" + "--strip-components=1"))))))))) + +(define covid19-pubseq-shepherd-service + (match-lambda + (($ <covid19-pubseq-configuration> package deploy-directory port) + (with-imported-modules (source-module-closure + '((gnu build shepherd) + (gnu system file-systems))) + (list (shepherd-service + (provision '(covid19-pubseq)) + (requirement '(networking)) + (modules '((gnu build shepherd) + (gnu system file-systems))) + ;(start #~(make-forkexec-constructor/container + (start #~(make-forkexec-constructor + (list + #$(file-append gunicorn "/bin/gunicorn") + (string-append "-blocalhost:" #$port) + "bh20simplewebuploader.main:app") + #:directory #$deploy-directory + #:log-file "/var/log/covid19-pubseq.log" + #:environment-variables + '("TMPDIR=/export/tmp" + ;; TODO: Don't hardcode python version! + "PYTHONPATH=/run/current-system/profile/lib/python3.8/site-packages") + ;#:mappings + ;(list (file-system-mapping + ; (source "/export/tmp") + ; (target source) + ; (writable? #t)) + ; (file-system-mapping + ; ;; TODO: Don't hardcode python version! + ; (source "/run/current-system/profile/lib/python3.8/site-packages") + ; (target source))) + )) + (stop #~(make-kill-destructor)))))))) + +(define covid19-pubseq-service-type + (service-type + (name 'covid19-pubseq) + (extensions + (list + (service-extension shepherd-root-service-type + covid19-pubseq-shepherd-service) + (service-extension activation-service-type + covid19-pubseq-activation-service) + (service-extension profile-service-type + (compose list + covid19-pubseq-configuration-package)))) + (default-value (covid19-pubseq-configuration)) + (description + "Run a COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver."))) + +(operating-system + (host-name "covid19-pubseq") + (timezone "Etc/UTC") + (locale "en_US.utf8") + + (bootloader (bootloader-configuration + (bootloader grub-bootloader) + (target "does-not-matter"))) + (file-systems %base-file-systems) + ;; No firmware for VMs. + (firmware '()) + ;; We don't need any packages inside the container. + (packages '()) + + (services (list (service covid19-pubseq-service-type)))) |