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authorEfraim Flashner2021-05-25 17:22:01 +0300
committerEfraim Flashner2021-05-25 17:22:01 +0300
commit1c9f28cf85aeee727d65a14f073fb92da7330a74 (patch)
treef21a62c6ec9ea165ce0f8cab1189f00b0232188d /gn/services/pluto.scm
parent8d8ad7f84236afaf5ae1d4b4bd9d51489da65301 (diff)
downloadguix-bioinformatics-1c9f28cf85aeee727d65a14f073fb92da7330a74.tar.gz
gn: visuals more progress
Diffstat (limited to 'gn/services/pluto.scm')
-rw-r--r--gn/services/pluto.scm55
1 files changed, 10 insertions, 45 deletions
diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm
index 3df804c..76a45c2 100644
--- a/gn/services/pluto.scm
+++ b/gn/services/pluto.scm
@@ -16,42 +16,21 @@
pluto-configuration?
(package pluto-configuration-package ; package
(default julia-visuals))
+ ;; TODO: Currently port 4343 is hardcoded in the package definition.
(port pluto-configuration-port ; integer
(default 80)))
(define %julia-account
(list (user-group
(name "julia")
- ;(system? #t)
- )
+ (system? #t))
(user-account
(name "julia")
(group "julia")
- ;(system? #t)
+ (system? #t)
(comment "Julia User")
(home-directory "/home/jovyan")
- ;(shell (file-append shadow "/sbin/nologin"))
- )))
-
-;(define pluto-activation
-; (match-lambda
-; (($ <ratspub-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 #$(file-append package "/userspub.sqlite") data_dir)
-; (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
+ (shell (file-append shadow "/sbin/nologin")))))
(define pluto-shepherd-service
(match-lambda
@@ -66,22 +45,15 @@
(gnu system file-systems)))
(start #~(make-forkexec-constructor/container
(list #$(file-append package "/runpluto.sh") #$port)
- ;; Needs to run from the directory it is located in.
- ;#:directory #$package
#:log-file "/var/log/pluto.log"
- ;; We don't need to set TMPDIR because we're inside a container.
#:user "julia"
#:group "julia"
- #:environment-variables
- '(;"JULIA_PROJECT=/home/jovyan"
- ;"JULIA_LOAD_PATH=/run/current-system/profile/share/julia/packages/"
- )
+ ;; This needs to exist. Unclear why.
+ #:environment-variables '()
#:mappings (list (file-system-mapping
(source "/home/jovyan")
(target source)
- (writable? #t))
- )
- ))
+ (writable? #t)))))
(stop #~(make-kill-destructor))))))))
(define pluto-service-type
@@ -91,13 +63,8 @@
(list
(service-extension shepherd-root-service-type
pluto-shepherd-service)
- ;(service-extension activation-service-type
- ; ratspub-activation)
(service-extension account-service-type
- (const %julia-account))
- ;; Make sure we get all the dependencies of julia-visuals.
- (service-extension profile-service-type
- (compose list pluto-configuration-package))))
+ (const %julia-account))))
(default-value (pluto-configuration))
(description
"Run a Pluto Jupyter Webserver.")))
@@ -118,9 +85,7 @@
;; (kernel linux-libre-vm)
;; No firmware for VMs.
(firmware '())
- (packages ;(list nss-certs)
- %base-packages
- )
+ (packages (list nss-certs))
(services (list (service pluto-service-type
(pluto-configuration
@@ -130,5 +95,5 @@
;; 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/pluto.scm --network
;; Docker instructions:
-;; docker load --input pluto-docker-image.tar.gz
+;; docker load --input guix-docker-image.tar.gz
;; docker run -d --privileged --net=host --name pluto guix