Merge branch 'main' into k8s-backend

form.yml

@@ -13,8 +13,6 @@ cluster: "my-k8s-cluster"
 form:
   - Rserver
   - Rapp
-  - extra_jupyter_args
-  - bc_queue
   - bc_num_hours
   - num_cores
   - num_mem
@@ -53,15 +51,13 @@ attributes:
       - [ "4.3.2", "R/4.3.2-foss-2023a" ]
       - [ "4.3.1", "R/4.3.1-foss-2023a" ]
       - [ "4.2.1", "R/4.2.1-gimkl-2022a" ]
-      - ["Bioconductor-3.17","R-bundle-Bioconductor/3.17-gimkl-2022a-R-4.3.1"] 
-      - ["R-Geo/4.3.2","R-Geo/4.3.2-foss-2023a"]
+      - ["Bioconductor-3.17", "R-bundle-Bioconductor/3.17-gimkl-2022a-R-4.3.1"]
+      - ["R-Geo/4.3.2", "R-Geo/4.3.2-foss-2023a"]
 
   # Any extra command line arguments to feed to the `jupyter notebook ...`
   # command that launches the Jupyter notebook within the batch job
 
   node: ""
-  bc_queue:
-    value: interactive
   bc_num_hours:
     max: 8
     min: 1

submit.yml.erb

@@ -13,7 +13,7 @@ script:
   native:
     container:
       name: "rstudio"
-      image: "ghcr.io/lbrick/nesi-docker-base/nesi-docker-base:0.7"
+      image: "ghcr.io/nesi/nesi-docker-base:v0.2.0"
       command: ["/bin/bash","-l","<%= staged_root %>/job_script_content.sh"]
       restart_policy: 'OnFailure'
       env:
@@ -67,4 +67,4 @@ script:
             CFG="$(hostname)-secret"
 
             kubectl get secret ${CFG} -o json | jq --arg key $KEY --arg value $VALUE '.data[$key] = $value'  | kubectl apply -f -
-          mount_path: '/opt/open_ondemand/helpers'
+          mount_path: '/opt/open_ondemand/helpers'

template/script.sh.erb

@@ -11,15 +11,8 @@ module load <%= context.Rserver %>
 # load R
 module load <%= context.Rapp %>
 
-# load additional Modules
-module load Python/3.11.6-foss-2023a
-
-#Only use the following if the os doesn't have pdflatex
-#module load TeXLive/2022
-
 # RStudioServer doesn't inherit "ulimit -s" from system config /etc/security/limits.d/custom.conf
 # Therefore, we are setting it here
-
 ulimit -s unlimited
 
 #