Upgrade spaceranger to 3.1.3

lilab-bcb · Feb 18, 2025 · f8e284b · f8e284b
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commit f8e284b
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Showing 2 changed files with 44 additions and 5 deletions.
diff --git a/docker/cellranger/7.1.0/Dockerfile b/docker/cellranger/7.1.0/Dockerfile
@@ -7,19 +7,19 @@ RUN apt-get update && \
 
 RUN 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 && \
     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-get install -y google-cloud-cli=415.0.0-0
+    apt-get update -y && apt-get install -y google-cloud-cli=509.0.0-0
 
-RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.9.18.zip" -o "awscliv2.zip" && \
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.24.0.zip" -o "awscliv2.zip" && \
     unzip awscliv2.zip && \
     ./aws/install && \
     rm awscliv2.zip
 
 RUN ln -s /usr/bin/python3 /usr/bin/python
 
 RUN python -m pip install --upgrade pip --no-cache-dir && \
-    python -m pip install pandas==1.5.3 --no-cache-dir && \
-    python -m pip install packaging==23.0 --no-cache-dir && \
-    python -m pip install stratocumulus==0.1.7 --no-cache-dir
+    python -m pip install pandas==2.2.3 --no-cache-dir && \
+    python -m pip install packaging==24.2 --no-cache-dir && \
+    python -m pip install stratocumulus==0.2.4 --no-cache-dir
 
 RUN mkdir /software
 ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software
@@ -32,3 +32,6 @@ RUN apt-get -qq -y autoremove && \
 RUN chmod a+rx /software/monitor_script.sh
 ENV PATH=/software:/software/cellranger-7.1.0:$PATH
 ENV TMPDIR=/tmp
+
+ENV CLOUDSDK_PYTHON=/usr/lib/google-cloud-sdk/platform/bundledpythonunix/bin/python
+ENV CLOUDSDK_GSUTIL_PYTHON=/usr/lib/google-cloud-sdk/platform/bundledpythonunix/bin/python
diff --git a/docker/spaceranger/3.1.3/Dockerfile b/docker/spaceranger/3.1.3/Dockerfile
@@ -0,0 +1,36 @@
+FROM debian:bookworm-slim
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y unzip build-essential dpkg-dev curl rsync gnupg procps python3 python3-pip python3-venv
+
+RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
+    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \
+    apt-get update -y && apt-get install -y google-cloud-cli=510.0.0-0
+
+ENV CLOUDSDK_PYTHON=/usr/lib/google-cloud-sdk/platform/bundledpythonunix/bin/python
+ENV CLOUDSDK_GSUTIL_PYTHON=/usr/lib/google-cloud-sdk/platform/bundledpythonunix/bin/python
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.24.6.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && \
+    ./aws/install && \
+    rm awscliv2.zip
+
+RUN python3 -m venv /software/python
+ENV PATH=/software/python/bin:$PATH
+
+RUN python -m pip install --upgrade pip --no-cache-dir && \
+    python -m pip install pandas==2.2.3 --no-cache-dir && \
+    python -m pip install packaging==24.2 --no-cache-dir && \
+    python -m pip install stratocumulus==0.2.4 --no-cache-dir
+
+ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software
+ADD spaceranger-3.1.3.tar.gz /software
+
+RUN apt-get -qq -y autoremove && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
+
+RUN chmod a+rx /software/monitor_script.sh
+ENV PATH=/software:/software/spaceranger-3.1.3:/usr/local/aws-cli/v2/current/bin:$PATH
+ENV TMPDIR=/tmp