diff --git a/form.yml b/form.yml index c03b658..4bd9867 100644 --- a/form.yml +++ b/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 diff --git a/submit.yml.erb b/submit.yml.erb index 2482571..08776d9 100644 --- a/submit.yml.erb +++ b/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' \ No newline at end of file + mount_path: '/opt/open_ondemand/helpers' diff --git a/template/script.sh.erb b/template/script.sh.erb index 3253e5f..95e833e 100755 --- a/template/script.sh.erb +++ b/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 #