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PD-2560: Add gsutil to snm3c Dockerfile #132

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PD-2560: Add gsutil to snm3c Dockerfile #132

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14cdf5a
Add gsutil
aawdeh Jul 19, 2024
3cc4d30
Add env variables for gsutil installation
aawdeh Jul 19, 2024
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24 changes: 16 additions & 8 deletions 3rd-party-tools/m3c-yap-hisat/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@ FROM --platform="linux/amd64" mambaorg/micromamba:0.23.0

WORKDIR /usr/gitc
RUN echo $PATH
ENV PATH="$PATH:/opt/conda/bin:/root/pkg/hisat-3n"
ENV GCLOUD_DIR="/opt/gcloud" \
GOOGLE_CLOUD_CLI_VERSION="397.0.0"
ENV PATH="/opt/conda/bin:/root/pkg/hisat-3n:$GCLOUD_DIR/google-cloud-sdk/bin:$PATH"
RUN echo $PATH

USER root
Expand All @@ -12,13 +14,13 @@ 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
Expand All @@ -29,7 +31,7 @@ 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
Expand All @@ -43,4 +45,10 @@ 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
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