Merge pull request #85 from kundajelab/consolidate-docker-layers

Consolidate docker layers

dockerfile

@@ -9,10 +9,11 @@ WORKDIR /scratch
 
 # Install some basic utilities
 RUN apt-get update --fix-missing && \
-    apt-get install -y wget bzip2 ca-certificates curl git
+    apt-get install -y --allow-unauthenticated wget bzip2 ca-certificates curl git jq libcairo2 libpango-1.0-0 libpangocairo-1.0-0 libgdk-pixbuf2.0-0 libffi-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # Install Google Cloud SDK
-RUN apt-get update && apt install -y --allow-unauthenticated wget
 RUN cd /opt/ && \
     wget https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-307.0.0-linux-x86_64.tar.gz && \
     tar xvfz google-cloud-sdk-307.0.0-linux-x86_64.tar.gz && \
@@ -27,26 +28,15 @@ RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linu
 # Enable Conda and alter bashrc so the Conda default environment is always activated
 RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
     echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
-    echo "conda activate base" >> ~/.bashrc
+    echo "conda activate base" >> ~/.bashrc && \
+    conda clean -tipy 
 
 # Attach Conda to PATH
 ENV PATH /opt/conda/bin:$PATH
 
 # Install SAMtools, BEDtools, and UCSC BedGraphToBigWig
 RUN conda install -y -c conda-forge -c bioconda samtools bedtools ucsc-bedgraphtobigwig pybigwig meme
 
-# Install jq
-RUN apt-get install -y jq
-RUN apt-get install -y libcairo2
-RUN apt-get install -y libpango-1.0-0
-RUN apt-get install -y libpangocairo-1.0-0
-RUN apt-get install -y libgdk-pixbuf2.0-0
-RUN apt-get install -y libffi-dev
-
-# Clean up after apt and conda
-RUN apt-get clean && rm -rf /var/lib/apt/lists/*
-RUN conda clean -tipy
-
 # Set environment variables for Python
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
@@ -56,10 +46,8 @@ RUN mkdir /scratch/chrombpnet
 COPY . /scratch/chrombpnet
 
 # need to upgrade pip for faster dependency resolution
-RUN pip install --upgrade pip 
-
-# Install any needed packages specified in requirements.txt
-RUN pip install -r /scratch/chrombpnet/requirements.txt
+RUN pip install --upgrade pip && \
+    pip install -r /scratch/chrombpnet/requirements.txt
 
 #Install chrombpnet itself
 WORKDIR /scratch