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ATpoint/Dockerfile_Parse_1-6-3

Created November 24, 2025 10:40
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Dockerfile to build a Docker image for the split-pipe preprocessing pipeline for Parse scRNA-seq data. Here Parse version 1.6.3 is assumes.
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Dockerfile_Parse_1-6-3
# Start from Miniconda which already contains conda and an appropriate pipeline version
FROM continuumio/miniconda3:25.3.1-1
WORKDIR /app
# That is downloaded from Parse which is behind a login for customers
COPY ParseBiosciences-Pipeline.1.6.3.zip .
# The gsub is encessary because inside docker there is no explicit sudo but the Parse script sudos a lot
RUN apt update && apt install -y unzip && \
unzip ParseBiosciences-Pipeline.1.6.3.zip && \
cd ParseBiosciences-Pipeline.1.6.3 && \
awk '{gsub("sudo ", ""); print}' install_dependencies.sh > install_dependencies_root.sh && \
bash install_dependencies_root.sh -y -i && \
pip install --no-cache-dir .
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