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Merge pull request #1020 from Layth17/master
Docker image to run pvacview on GCP
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,31 @@ | ||
| FROM rocker/shiny-verse | ||
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| RUN R -e "install.packages(c('shiny',\ | ||
| 'shinyjs',\ | ||
| 'shinythemes',\ | ||
| 'plotly', \ | ||
| 'RMySQL',\ | ||
| 'ggplot2',\ | ||
| 'DT',\ | ||
| 'reshape2',\ | ||
| 'jsonlite',\ | ||
| 'tibble',\ | ||
| 'tidyr',\ | ||
| 'plyr',\ | ||
| 'dplyr',\ | ||
| 'stringr', \ | ||
| 'shinydashboard', \ | ||
| 'shinydashboardPlus', \ | ||
| 'shinycssloaders', \ | ||
| 'fresh', \ | ||
| 'RCurl' ), repos='https://cran.rstudio.com/')" | ||
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| RUN R -e "devtools::install_github('eclarke/ggbeeswarm', ref='v0.6.1')" | ||
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| RUN rm -rf /srv/shiny-server/* | ||
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| COPY . /srv/shiny-server/ | ||
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| EXPOSE 3333 | ||
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| CMD ["R", "-e", "shiny::runApp('/srv/shiny-server/', port = 3333, host='0.0.0.0')"] |
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| @@ -0,0 +1,137 @@ | ||
| IMAGE_NAME="pvacview" | ||
| TAG_NAME="latest" # do not change this unless you have looked at how your service fetches the tag | ||
| REGION="us-central1" | ||
| LAB="griffith-lab" # also the project name | ||
| REPO="shiny-apps" | ||
| SERVICE_NAME="pvacview" | ||
| SERVICE_TAG=$2 # format like: v1-0-0 | ||
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| # script | ||
| COMMAND=$1 # init or update | ||
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| function show_help { | ||
| echo "usage: sh gcloud_service.sh COMMAND <TAG>" | ||
| echo "" | ||
| echo "commands:" | ||
| echo " init Creates a new service in Cloud Run." | ||
| echo " update updates an existing service in Cloud Run." | ||
| echo "" | ||
| echo "arguments:" | ||
| echo " <TAG> Positional argument that tags the revision/release of the service (example: v1-0-0)." | ||
| echo "" | ||
| } | ||
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| function validate { | ||
| # check if Docker is running | ||
| if ! docker info >/dev/null 2>&1; then | ||
| echo "ERROR: Docker does not appear to be running. Please start Docker." | ||
| # Exit with a non-zero status to indicate that Docker isn't running | ||
| exit 1 | ||
| fi | ||
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| # check if you are logged in | ||
| if [[ -z $(gcloud auth list --filter=status:ACTIVE --format="value(account)") ]]; then | ||
| echo "<< Please log in.>>" | ||
| gcloud auth login | ||
| else | ||
| echo "<< [Alread logged in]: Welcome, $(gcloud auth list --filter=status:ACTIVE --format="value(account)") >>" | ||
| fi | ||
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| # check if user is allowed to push to Artifact Registry | ||
| if [[ -z $(cat ~/.docker/config.json | grep "\"$REGION-docker.pkg.dev\": \"gcloud\"") ]]; then | ||
| echo "<< Attempting to Authenticate before pushing to Artifact Registry. >>" | ||
| gcloud auth configure-docker $REGION-docker.pkg.dev | ||
| else | ||
| echo "<< Allowed to push to Artifact Registry >>" | ||
| fi | ||
| } | ||
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| function build_and_push_image { | ||
| # build the image | ||
| docker build . --tag $REGION-docker.pkg.dev/$LAB/$REPO/$IMAGE_NAME:$TAG_NAME | ||
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| # Check the exit code of the docker build command | ||
| if [ $? -ne 0 ]; then | ||
| echo "Error: Docker build failed" | ||
| exit 1 | ||
| fi | ||
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| # push the image | ||
| docker push $REGION-docker.pkg.dev/$LAB/$REPO/$IMAGE_NAME:$TAG_NAME | ||
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| # Check the exit code of the docker push command | ||
| if [ $? -ne 0 ]; then | ||
| echo "Error: Docker push failed" | ||
| exit 1 | ||
| fi | ||
| } | ||
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| function init { | ||
| build_and_push_image | ||
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| # deploy: https://cloud.google.com/sdk/gcloud/reference/run/deploy | ||
| gcloud --project $LAB run deploy $SERVICE_NAME \ | ||
| --image $REGION-docker.pkg.dev/$LAB/$REPO/$IMAGE_NAME:$TAG_NAME \ | ||
| --port=3333 \ | ||
| --min-instances=0 \ | ||
| --max-instances=100 \ | ||
| --memory=2Gi \ | ||
| --cpu=4 \ | ||
| --timeout=300 \ | ||
| --allow-unauthenticated \ | ||
| --update-env-vars KEY=VALUE --revision-suffix $SERVICE_TAG | ||
| } | ||
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| function update { | ||
| # check SERVICE_TAG does not already exist | ||
| TAGS=$(gcloud run revisions list --project $LAB --service $SERVICE_NAME --format="value(REVISION)") | ||
| if [[ $TAGS =~ $SERVICE_TAG ]]; then | ||
| echo "ERROR: The Service \"$SERVICE_NAME\" already has revision $SERVICE_TAG. Please use a new tag." | ||
| exit 1 | ||
| fi | ||
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| # set region; updating service will ask for region if this is not set | ||
| if [[ $(gcloud config get-value run/region) != "$REGION" ]]; then | ||
| echo "<< Upadting property [run/region] to $REGION >>" | ||
| gcloud config set run/region $REGION | ||
| fi | ||
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| build_and_push_image | ||
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| # update service | ||
| if [[ -z $(gcloud --project $LAB run services list | grep -w $SERVICE_NAME) ]]; then | ||
| echo "<<ERROR: Your service does not exist. You must initialize it first. >>" | ||
| else | ||
| gcloud --project $LAB run services update $SERVICE_NAME --update-env-vars KEY=VALUE --revision-suffix $SERVICE_TAG | ||
| fi | ||
| } | ||
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| if [[ ($COMMAND != "init") && ($COMMAND != "update")]]; then | ||
| show_help | ||
| echo "ERROR: invalid command." | ||
| exit 1 | ||
| else | ||
| validate | ||
| case $COMMAND in | ||
| "init") | ||
| init | ||
| ;; | ||
| "update") | ||
| update | ||
| ;; | ||
| esac | ||
| fi | ||
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