diff --git a/3rd-party-tools/m3c-yap-hisat/Dockerfile b/3rd-party-tools/m3c-yap-hisat/Dockerfile index 20f56446..96850bec 100644 --- a/3rd-party-tools/m3c-yap-hisat/Dockerfile +++ b/3rd-party-tools/m3c-yap-hisat/Dockerfile @@ -12,13 +12,13 @@ USER root # docker build --build-arg gcp=true -t mapping-gcp:tag . ARG gcp RUN if [ "$gcp" = "true" ] ; then \ - apt-get update && \ - apt-get install -y curl gnupg && \ + apt-get update; \ + apt-get install -y curl gnupg; \ echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | \ - tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \ + tee -a /etc/apt/sources.list.d/google-cloud-sdk.list; \ curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | \ - apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \ - apt-get update -y && \ + apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - ; \ + apt-get update -y; \ apt-get install google-cloud-sdk -y; \ else echo 'no gcp install'; \ fi @@ -29,7 +29,7 @@ RUN apt-get update; \ apt-get install -y build-essential COPY --chown=$MAMBA_USER:$MAMBA_USER hisat3n_env.yml /tmp/hisat3n_env.yml -RUN micromamba install -y -f /tmp/hisat3n_env.yml && \ +RUN micromamba install -y -f /tmp/hisat3n_env.yml; \ micromamba clean --all --yes ARG MAMBA_DOCKERFILE_ACTIVATE=1 @@ -43,4 +43,10 @@ RUN mkdir -p ~/pkg; \ git checkout -b hisat-3n origin/hisat-3n; \ make; \ echo 'export PATH=$HOME/pkg/hisat-3n:$PATH' >> ~/.bashrc; \ - source ~/.bashrc + source ~/.bashrc; \ + # get gsutil + mkdir -p $GCLOUD_DIR; \ + curl -so $HOME/google-cloud-cli.tar.gz https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-cli-${GOOGLE_CLOUD_CLI_VERSION}-linux-x86_64.tar.gz; \ + tar -xzf $HOME/google-cloud-cli.tar.gz -C $GCLOUD_DIR; \ + .$GCLOUD_DIR/google-cloud-sdk/install.sh --usage-reporting false; \ + rm $HOME/google-cloud-cli.tar.gz; \