diff options
Diffstat (limited to 'gn/services')
| -rw-r--r-- | gn/services/bh20-seq-resource-container.scm | 12 | ||||
| -rw-r--r-- | gn/services/databases.scm | 5 | ||||
| -rw-r--r-- | gn/services/genome-browser.scm | 2 | ||||
| -rw-r--r-- | gn/services/pluto.scm | 14 |
4 files changed, 25 insertions, 8 deletions
diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm index cb77cdb..e0eccf7 100644 --- a/gn/services/bh20-seq-resource-container.scm +++ b/gn/services/bh20-seq-resource-container.scm @@ -5,6 +5,7 @@ (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) @@ -14,7 +15,7 @@ make-covid19-pubseq-configuration covid19-pubseq-configuration? (package covid19-pubseq-configuration-package ; package - (default bh20-seq-resource)) + (default bh20-seq-resource-for-service)) (deploy-directory covid19-pubseq-deploy-directory ; string (default "/srv/http")) (port covid19-pubseq-configuration-port ; string @@ -58,9 +59,10 @@ #:directory #$deploy-directory #:log-file "/var/log/covid19-pubseq.log" #:environment-variables + ;(let (pyversion (python-version (@ (gnu packages python) python))) '("TMPDIR=/export/tmp" - ;; TODO: Don't hardcode python version! - "PYTHONPATH=/run/current-system/profile/lib/python3.8/site-packages") + "PYTHONPATH=/run/current-system/profile/lib/python3.9/site-packages") + ; (string-append "PYTHONPATH=/run/current-system/profile/lib/python" pyversion "/site-packages"))) ;#:mappings ;(list (file-system-mapping ; (source "/export/tmp") @@ -68,7 +70,7 @@ ; (writable? #t)) ; (file-system-mapping ; ;; TODO: Don't hardcode python version! - ; (source "/run/current-system/profile/lib/python3.8/site-packages") + ; (source "/run/current-system/profile/lib/python3.9/site-packages") ; (target source))) )) (stop #~(make-kill-destructor)))))))) @@ -104,3 +106,5 @@ (packages '()) (services (list (service covid19-pubseq-service-type)))) + +;; guix system container /home/shepherd/guix-bioinformatics/gn/services/bh20-seq-resource-container.scm --share=/export/tmp=/export/tmp --network diff --git a/gn/services/databases.scm b/gn/services/databases.scm index 2b2b225..937aa9e 100644 --- a/gn/services/databases.scm +++ b/gn/services/databases.scm @@ -33,6 +33,8 @@ (default "localhost")) (server-port virtuoso-configuration-server-port (default 1111)) + (dirs-allowed virtuoso-dirs-allowed + (default "/var/genenetwork/virtuoso-data")) (number-of-buffers virtuoso-configuration-number-of-buffers (default #f)) (maximum-dirty-buffers virtuoso-configuration-maximum-dirty-buffers @@ -84,6 +86,9 @@ (format port "ServerPort = ~a:~a~%" #$(virtuoso-configuration-server-ip config) #$(virtuoso-configuration-server-port config))) + (when #$(virtuoso-dirs-allowed config) + (format port "DirsAllowed = ~a~%" + #$(virtuoso-dirs-allowed config))) (when #$(virtuoso-configuration-number-of-buffers config) (format port "NumberOfBuffers = ~a~%" #$(virtuoso-configuration-number-of-buffers config))) diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm index 2d14a42..e350674 100644 --- a/gn/services/genome-browser.scm +++ b/gn/services/genome-browser.scm @@ -130,7 +130,7 @@ (program (file-append ucsc-genome-browser "/bin/gfServer")) (arguments '("gfServer" "dynserver" "/gbdb"))))))) - (syslog-service) ; needed by inetd + (service syslog-service-type) ; needed by inetd (service httpd-service-type (httpd-configuration (config diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm index d137314..720b769 100644 --- a/gn/services/pluto.scm +++ b/gn/services/pluto.scm @@ -44,16 +44,20 @@ (modules '((gnu build shepherd) (gnu system file-systems))) (start #~(make-forkexec-constructor/container - (list #$(file-append package "/runpluto.sh") #$port) + ;(list #$(file-append package "/runpluto.sh") #$port) + (list #$(file-append package "/runpluto")) #:log-file "/var/log/pluto.log" #:user "julia" #:group "julia" - ;; This needs to exist. Unclear why. + ;; This prevents the service from using /root as $HOME. #:environment-variables '() #:mappings (list (file-system-mapping (source "/home/jovyan") (target source) - (writable? #t))))) + (writable? #t)) + (file-system-mapping + (source "/etc/ssl") + (target source))))) (stop #~(make-kill-destructor)))))))) (define pluto-service-type @@ -86,6 +90,10 @@ ;; No firmware for VMs. (firmware '()) (packages (list nss-certs)) + ;; For testing + ;(packages (cons* nss-certs %base-packages)) + + (setuid-programs '()) (services (list (service pluto-service-type (pluto-configuration |