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-rw-r--r--gn/services/bh20-seq-resource-container.scm106
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
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+(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))))