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authorShepherd on Tux022024-06-20 08:37:15 -0500
committerShepherd on Tux022024-06-20 08:37:15 -0500
commitfe5fd5cb23907f8e37edafda96bafa608a3e0e7f (patch)
tree0b4cec2038dde07fe26f1c6882369f36a9545a19 /gn/services
parentf0f8dc84eca7088177797f84db05314537615c77 (diff)
parent0362ee068a39ce9a5fd6f0fba9cd5586211f07f1 (diff)
downloadguix-bioinformatics-fe5fd5cb23907f8e37edafda96bafa608a3e0e7f.tar.gz
Merge branch 'master' of /home/git/public/guix-bioinformatics
Diffstat (limited to 'gn/services')
-rw-r--r--gn/services/bh20-seq-resource-container.scm110
-rw-r--r--gn/services/pluto.scm17
2 files changed, 5 insertions, 122 deletions
diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm
deleted file mode 100644
index e0eccf7..0000000
--- a/gn/services/bh20-seq-resource-container.scm
+++ /dev/null
@@ -1,110 +0,0 @@
-(define-module (gn services bh20-seq-resource-container))
-
-(use-modules (gnu)
- (gn packages bioinformatics)
- (guix modules)
- ((guix packages) #:select (package-source))
- (guix records)
- (guix build-system python) ; for python-version from guix/build/python-build-system.scm
- (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-for-service))
- (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
- ;(let (pyversion (python-version (@ (gnu packages python) python)))
- '("TMPDIR=/export/tmp"
- "PYTHONPATH=/run/current-system/profile/lib/python3.9/site-packages")
- ; (string-append "PYTHONPATH=/run/current-system/profile/lib/python" pyversion "/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/python3.9/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)
- (targets '("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))))
-
-;; guix system container /home/shepherd/guix-bioinformatics/gn/services/bh20-seq-resource-container.scm --share=/export/tmp=/export/tmp --network
diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm
index 720b769..420e2cf 100644
--- a/gn/services/pluto.scm
+++ b/gn/services/pluto.scm
@@ -43,21 +43,14 @@
(requirement '(networking))
(modules '((gnu build shepherd)
(gnu system file-systems)))
- (start #~(make-forkexec-constructor/container
- ;(list #$(file-append package "/runpluto.sh") #$port)
- (list #$(file-append package "/runpluto"))
+ (start #~(make-forkexec-constructor
+ '(#$(file-append package "/bin/runsliderserver"))
#:log-file "/var/log/pluto.log"
#:user "julia"
#:group "julia"
- ;; This prevents the service from using /root as $HOME.
- #:environment-variables '()
- #:mappings (list (file-system-mapping
- (source "/home/jovyan")
- (target source)
- (writable? #t))
- (file-system-mapping
- (source "/etc/ssl")
- (target source)))))
+ #:environment-variables
+ (list "SSL_CERT_DIR=/etc/ssl/certs"
+ "SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt")))
(stop #~(make-kill-destructor))))))))
(define pluto-service-type