diff --git a/docker/analysis-tools/Dockerfile b/docker/analysis-tools/Dockerfile index 0759050f0..8e2e86c57 100644 --- a/docker/analysis-tools/Dockerfile +++ b/docker/analysis-tools/Dockerfile @@ -36,10 +36,12 @@ RUN apt update && apt install -y \ libboost-all-dev \ libbz2-dev \ liblzma-dev \ + lsb-release \ r-base \ r-base-core \ r-base-dev \ samtools \ + sudo \ wget \ zlib1g-dev @@ -57,6 +59,7 @@ RUN pip3 install \ tables==3.4.2 \ google-cloud-storage \ git+git://github.com/HumanCellAtlas/pipeline-tools.git + # Fix cannot import name 'opentype' error RUN pip3 install --upgrade google-auth-oauthlib @@ -68,14 +71,17 @@ RUN Rscript -e "install.packages('ggplot2')" RUN Rscript -e "install.packages('googleCloudStorageR')" # Mount Google Cloud secret key -ADD broad-dsde-mint-dev-ed8cc09c48e5.json /usr/secrets/broad-dsde-mint-dev-ed8cc09c48e5.json +ADD broad-dsde-mint-dev-testR.json /usr/secrets/broad-dsde-mint-dev-testR.json # Set the environment variable for Python -ENV GOOGLE_APPLICATION_CREDENTIALS=/usr/secrets/broad-dsde-mint-dev-ed8cc09c48e5.json +ENV GOOGLE_APPLICATION_CREDENTIALS=/usr/secrets/broad-dsde-mint-dev-testR.json # Set the environment variable for R -ENV GCS_AUTH_FILE=/usr/secrets/broad-dsde-mint-dev-ed8cc09c48e5.json - - +ENV GCS_AUTH_FILE=$GOOGLE_APPLICATION_CREDENTIALS +# Install gcloud components +RUN curl -sSL https://sdk.cloud.google.com > /tmp/gcl && bash /tmp/gcl --install-dir=/usr/gcloud --disable-prompts +# Configure gcloud +ENV PATH $PATH:/usr/gcloud/google-cloud-sdk/bin +RUN gcloud auth activate-service-account --key-file=$GCS_AUTH_FILE