From 51def1870a55ba2f5c3bec855684bf835da9628e Mon Sep 17 00:00:00 2001
From: Arkadii Yakovets <ark@ccdatalab.org>
Date: Wed, 27 Sep 2023 13:58:45 -0700
Subject: [PATCH] Update docker files: use heredocs syntax

Update downloaders image aspera path.
---
 api/dockerfiles/Dockerfile.api               |  12 +-
 api/dockerfiles/Dockerfile.api_base          |  25 +++--
 api/dockerfiles/Dockerfile.api_local         |   2 +
 common/dockerfiles/Dockerfile.base           | 103 ++++++++---------
 foreman/dockerfiles/Dockerfile.foreman       |  16 +--
 workers/dockerfiles/Dockerfile.affymetrix    |   3 +-
 workers/dockerfiles/Dockerfile.compendia     | 110 +++++++++----------
 workers/dockerfiles/Dockerfile.downloaders   |  26 +++--
 workers/dockerfiles/Dockerfile.illumina      |   3 +-
 workers/dockerfiles/Dockerfile.no_op         |  13 ++-
 workers/dockerfiles/Dockerfile.salmon        |  42 ++++---
 workers/dockerfiles/Dockerfile.smasher       |   3 +-
 workers/dockerfiles/Dockerfile.transcriptome |  29 +++--
 13 files changed, 197 insertions(+), 190 deletions(-)

diff --git a/api/dockerfiles/Dockerfile.api b/api/dockerfiles/Dockerfile.api
index bbdf1af3e..292d1149a 100644
--- a/api/dockerfiles/Dockerfile.api
+++ b/api/dockerfiles/Dockerfile.api
@@ -5,10 +5,14 @@ FROM $DOCKERHUB_REPO/dr_api_base:$SYSTEM_VERSION
 # Fail in case of an error at any stage in the pipe.
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
-RUN pip install --ignore-installed --no-cache-dir uwsgi && \
-    chmod +x /home/user/collect_and_run_uwsgi.sh && \
-    mkdir -p /tmp/www/static && \
-    chown user /tmp/www/static
+RUN <<EOF
+pip install --ignore-installed --no-cache-dir uwsgi
+chmod +x /home/user/collect_and_run_uwsgi.sh
+mkdir -p /tmp/www/static
+chown user /tmp/www/static
+EOF
+
+ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
 USER user
 
diff --git a/api/dockerfiles/Dockerfile.api_base b/api/dockerfiles/Dockerfile.api_base
index 44bf4c787..3503db769 100644
--- a/api/dockerfiles/Dockerfile.api_base
+++ b/api/dockerfiles/Dockerfile.api_base
@@ -4,27 +4,28 @@ FROM python:3.8.5-buster
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 # Install gcc and libpq-dev for psycopg2.
-RUN apt-get update -qq && \
-    apt-get install -y \
-        gcc \
-        libpq-dev && \
-    groupadd user && \
-    useradd --create-home --home-dir /home/user -g user user
+RUN <<EOF
+apt-get update -qq
+apt-get install -y \
+    gcc \
+    libpq-dev
+groupadd user
+useradd --create-home --home-dir /home/user -g user user
+EOF
 
 WORKDIR /home/user
 
 COPY api/requirements.txt .
-RUN pip install --upgrade pip && \
-    pip install --ignore-installed --no-cache-dir -r requirements.txt
+RUN <<EOF
+pip install --upgrade pip
+pip install --ignore-installed --no-cache-dir -r requirements.txt
+EOF
 
 COPY common/dist/data-refinery-common-* common/
-RUN pip install --ignore-installed \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip install --ignore-installed common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY api/ .
 COPY config/ config/
 COPY setup.cfg .
 
-ENV SYSTEM_VERSION=$SYSTEM_VERSION
-
 ENTRYPOINT []
diff --git a/api/dockerfiles/Dockerfile.api_local b/api/dockerfiles/Dockerfile.api_local
index 38cd1e5b7..c0ddb9846 100644
--- a/api/dockerfiles/Dockerfile.api_local
+++ b/api/dockerfiles/Dockerfile.api_local
@@ -5,6 +5,8 @@ FROM $DOCKERHUB_REPO/dr_api_base:$SYSTEM_VERSION
 # Fail in case of an error at any stage in the pipe.
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
+ENV SYSTEM_VERSION=$SYSTEM_VERSION
+
 USER user
 
 EXPOSE 8000
diff --git a/common/dockerfiles/Dockerfile.base b/common/dockerfiles/Dockerfile.base
index ef5d13c3b..ad21342e6 100644
--- a/common/dockerfiles/Dockerfile.base
+++ b/common/dockerfiles/Dockerfile.base
@@ -12,57 +12,58 @@ ENV DEBIAN_FRONTEND=noninteractive
 # For whatever reason this worked and 'en_US.UTF-8' did not.
 ENV LANG=C.UTF-8
 
-RUN apt-get update && \
-    apt-get install --no-install-recommends -y software-properties-common && \
-    add-apt-repository ppa:apt-fast/stable && \
-    add-apt-repository ppa:deadsnakes/ppa && \
-    add-apt-repository ppa:savoury1/llvm-defaults-10 && \
-    apt-get update -qq && \
-    apt-get install --no-install-recommends -y \
-        apt-fast \
-        apt-transport-https \
-        gpg-agent && \
-    apt-fast update -qq && apt-fast install -y \
-        build-essential \
-        cmake \
-        curl \
-        cython \
-        cython3 \
-        ed \
-        file \
-        git \
-        libcairo-dev \
-        libcurl4-gnutls-dev \
-        libedit-dev \
-        libfreetype6-dev \
-        libfribidi-dev \
-        libgit2-dev \
-        libharfbuzz-dev \
-        libjpeg-dev \
-        libpng-dev \
-        libpq-dev \
-        libssl-dev \
-        libtiff5-dev \
-        libxml2-dev \
-        llvm-10-dev \
-        lsb-release \
-        mercurial \
-        pkg-config \
-        python3-pip \
-        python3-pybind11 \
-        python3.8 \
-        python3.8-dev \
-        r-base-core \
-        wget && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* && \
-    ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config && \
-    update-alternatives --install \
-        /usr/bin/python3 python3 /usr/bin/python3.8 1 && \
-    pip3 install --upgrade pip setuptools && \
-    groupadd user && \
-    useradd --create-home --home-dir /home/user/ -g user user && \
-    chown -R user /home/user/
+RUN <<EOF
+apt-get update
+apt-get install --no-install-recommends -y software-properties-common
+add-apt-repository ppa:apt-fast/stable
+add-apt-repository ppa:deadsnakes/ppa
+add-apt-repository ppa:savoury1/llvm-defaults-10
+apt-get update -qq
+apt-get install --no-install-recommends -y \
+    apt-fast \
+    apt-transport-https \
+    gpg-agent && \
+apt-fast update -qq && apt-fast install -y \
+    build-essential \
+    cmake \
+    curl \
+    cython \
+    cython3 \
+    ed \
+    file \
+    git \
+    libcairo-dev \
+    libcurl4-gnutls-dev \
+    libedit-dev \
+    libfreetype6-dev \
+    libfribidi-dev \
+    libgit2-dev \
+    libharfbuzz-dev \
+    libjpeg-dev \
+    libpng-dev \
+    libpq-dev \
+    libssl-dev \
+    libtiff5-dev \
+    libxml2-dev \
+    llvm-10-dev \
+    lsb-release \
+    mercurial \
+    pkg-config \
+    python3-pip \
+    python3-pybind11 \
+    python3.8 \
+    python3.8-dev \
+    r-base-core \
+    wget
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config
+update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
+pip3 install --upgrade pip setuptools
+groupadd user
+useradd --create-home --home-dir /home/user/ -g user user
+chown -R user /home/user/
+EOF
 
 ENV R_LIBS=/usr/local/lib/R/site-library
 
diff --git a/foreman/dockerfiles/Dockerfile.foreman b/foreman/dockerfiles/Dockerfile.foreman
index 026f5159f..baf0cad7d 100644
--- a/foreman/dockerfiles/Dockerfile.foreman
+++ b/foreman/dockerfiles/Dockerfile.foreman
@@ -8,17 +8,17 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 WORKDIR /home/user
 
 COPY foreman/requirements.txt .
-RUN mkdir -p data/microarray && \
-    wget -q https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz \
-        -O data/microarray/GEOmetadb.sqlite.gz && \
-    gunzip data/microarray/GEOmetadb.sqlite.gz && \
-    chmod 644 data/microarray/GEOmetadb.sqlite && \
-    pip3 install --ignore-installed --no-cache-dir -r requirements.txt
+RUN <<EOF
+mkdir -p data/microarray
+wget -q https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz -O data/microarray/GEOmetadb.sqlite.gz
+gunzip data/microarray/GEOmetadb.sqlite.gz
+chmod 644 data/microarray/GEOmetadb.sqlite
+pip3 install --ignore-installed --no-cache-dir -r requirements.txt
+EOF
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY foreman/ .
diff --git a/workers/dockerfiles/Dockerfile.affymetrix b/workers/dockerfiles/Dockerfile.affymetrix
index 4d6482afe..478d377a5 100644
--- a/workers/dockerfiles/Dockerfile.affymetrix
+++ b/workers/dockerfiles/Dockerfile.affymetrix
@@ -19,8 +19,7 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .
diff --git a/workers/dockerfiles/Dockerfile.compendia b/workers/dockerfiles/Dockerfile.compendia
index dd3352e8a..e4f3cf557 100644
--- a/workers/dockerfiles/Dockerfile.compendia
+++ b/workers/dockerfiles/Dockerfile.compendia
@@ -15,53 +15,54 @@ ENV LANG=C.UTF-8
 
 # RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
 # via https://github.com/ilikenwf/apt-fast/issues/85#issuecomment-261640099
-RUN echo debconf apt-fast/maxdownloads string 16 | debconf-set-selections && \
-    echo debconf apt-fast/dlflag boolean true | debconf-set-selections && \
-    echo debconf apt-fast/aptmanager string apt-get | debconf-set-selections && \
-    echo 'tzdata tzdata/Areas select Etc' | debconf-set-selections && \
-    echo 'tzdata tzdata/Zones/Etc select UTC' | debconf-set-selections && \
-    apt-get update -qq && \
-    apt-get install --no-install-recommends -y software-properties-common && \
-    add-apt-repository ppa:apt-fast/stable && \
-    add-apt-repository ppa:deadsnakes/ppa && \
-    add-apt-repository ppa:savoury1/llvm-defaults-10 && \
-    apt-get update -qq && \
-    apt-get install --no-install-recommends -y apt-fast apt-transport-https gpg-agent tzdata && \
-    apt-fast update -qq && \
-    apt-fast install -y \
-        build-essential \
-        cmake \
-        curl \
-        cython3 \
-        ed \
-        gfortran \
-        git \
-        libblas-dev \
-        libcairo-dev \
-        libcurl4-openssl-dev \
-        libedit-dev \
-        liblapack-dev \
-        libpq-dev \
-        libssl-dev \
-        libxml2-dev \
-        llvm-10-dev \
-        lsb-release \
-        mercurial \
-        pkg-config \
-        python3-pip \
-        python3-pybind11 \
-        python3.8 \
-        python3.8-dev \
-        r-base-core \
-        wget && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* && \
-    ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config && \
-    update-alternatives --install /usr/bin/python3 python3 \
-        /usr/bin/python3.8 1 && \
-    pip3 install --upgrade pip setuptools && \
-    groupadd user && \
-    useradd --create-home --home-dir /home/user -g user user
+RUN <<EOF
+echo debconf apt-fast/maxdownloads string 16 | debconf-set-selections
+echo debconf apt-fast/dlflag boolean true | debconf-set-selections
+echo debconf apt-fast/aptmanager string apt-get | debconf-set-selections
+echo 'tzdata tzdata/Areas select Etc' | debconf-set-selections
+echo 'tzdata tzdata/Zones/Etc select UTC' | debconf-set-selections
+apt-get update -qq
+apt-get install --no-install-recommends -y software-properties-common
+add-apt-repository ppa:apt-fast/stable
+add-apt-repository ppa:deadsnakes/ppa
+add-apt-repository ppa:savoury1/llvm-defaults-10
+apt-get update -qq
+apt-get install --no-install-recommends -y apt-fast apt-transport-https gpg-agent tzdata
+apt-fast update -qq
+apt-fast install -y \
+    build-essential \
+    cmake \
+    curl \
+    cython3 \
+    ed \
+    gfortran \
+    git \
+    libblas-dev \
+    libcairo-dev \
+    libcurl4-openssl-dev \
+    libedit-dev \
+    liblapack-dev \
+    libpq-dev \
+    libssl-dev \
+    libxml2-dev \
+    llvm-10-dev \
+    lsb-release \
+    mercurial \
+    pkg-config \
+    python3-pip \
+    python3-pybind11 \
+    python3.8 \
+    python3.8-dev \
+    r-base-core \
+    wget
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config
+update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
+pip3 install --upgrade pip setuptools
+groupadd user
+useradd --create-home --home-dir /home/user -g user user
+EOF
 
 WORKDIR /home/user
 
@@ -78,17 +79,16 @@ COPY workers/data_refinery_workers/processors/requirements.txt requirements.txt
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Install phantomjs.
-RUN wget -q "https://bitbucket.org/ariya/phantomjs/downloads/\
-phantomjs-2.1.1-linux-x86_64.tar.bz2" && \
-    tar xvjf phantomjs-2.1.1-linux-x86_64.tar.bz2 -C /usr/local/share/ && \
-    ln -s /usr/local/share/phantomjs-2.1.1-linux-x86_64/bin/phantomjs \
-        /usr/local/bin/ && \
-    rm phantomjs-2.1.1-linux-x86_64.tar.bz2
+RUN <<EOF
+wget -q https://bitbucket.org/ariya/phantomjs/downloads/phantomjs-2.1.1-linux-x86_64.tar.bz2
+tar xvjf phantomjs-2.1.1-linux-x86_64.tar.bz2 -C /usr/local/share/
+ln -s /usr/local/share/phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin/
+rm phantomjs-2.1.1-linux-x86_64.tar.bz2
+EOF
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY config/ config/
diff --git a/workers/dockerfiles/Dockerfile.downloaders b/workers/dockerfiles/Dockerfile.downloaders
index decf0cc80..1d0e65b30 100644
--- a/workers/dockerfiles/Dockerfile.downloaders
+++ b/workers/dockerfiles/Dockerfile.downloaders
@@ -15,29 +15,33 @@ COPY workers/data_refinery_workers/downloaders/requirements.txt .
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Install Aspera.
-# Disable IPv6 to avoid "Cannot assign requested address" error.
-RUN mkdir -m 700 ~/.gnupg/ && \
-    echo "disable-ipv6" >> ~/.gnupg/dirmngr.conf && \
-    gpg --keyserver keyserver.ubuntu.com --recv-keys \
-        409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB && \
-    curl -sSL https://get.rvm.io | bash -s stable --ruby --gems=aspera-cli
+RUN <<EOF
+gpg --keyserver keyserver.ubuntu.com --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
+curl -sSL https://get.rvm.io | bash -s -- stable --gems=aspera-cli --path /home/user/rvm --ruby
+EOF
 
 USER user
-RUN . /usr/local/rvm/scripts/rvm && \
-    ascli conf ascp install
+
+RUN <<EOF
+mkdir -m 700 ~.gnupg/
+# Disable IPv6 to avoid "Cannot assign requested address" error.
+echo "disable-ipv6" >> ~.gnupg/dirmngr.conf
+. /home/user/rvm/scripts/rvm
+ascli conf ascp install
+EOF
+
 USER root
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .
 
 RUN rm -rf /root/.cache/*
 
-ENV PATH="$PATH:/home/user/.aspera/ascli/sdk"
+ENV PATH="$PATH:/home/user/.aspera/sdk"
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
 USER user
diff --git a/workers/dockerfiles/Dockerfile.illumina b/workers/dockerfiles/Dockerfile.illumina
index 5748788d9..54ac5539a 100644
--- a/workers/dockerfiles/Dockerfile.illumina
+++ b/workers/dockerfiles/Dockerfile.illumina
@@ -16,8 +16,7 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .
diff --git a/workers/dockerfiles/Dockerfile.no_op b/workers/dockerfiles/Dockerfile.no_op
index a9ffe09dd..67cf380be 100644
--- a/workers/dockerfiles/Dockerfile.no_op
+++ b/workers/dockerfiles/Dockerfile.no_op
@@ -18,18 +18,19 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 RUN mkdir -p gene_indexes
 WORKDIR /home/user/gene_indexes
 ENV ID_REFINERY_URL=https://zenodo.org/record/1410647/files/all_1536267482.zip
-RUN curl -O $ID_REFINERY_URL && \
-    echo $ID_REFINERY_URL > /etc/identifier_refinery_url && \
-    unzip *.zip && \
-    rm *.zip
+RUN <<EOF
+curl -O $ID_REFINERY_URL
+echo $ID_REFINERY_URL > /etc/identifier_refinery_url
+unzip *.zip
+rm *.zip
+EOF
 # End Noop-specific.
 
 WORKDIR /home/user
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .
diff --git a/workers/dockerfiles/Dockerfile.salmon b/workers/dockerfiles/Dockerfile.salmon
index ec2f49971..4a103f8b2 100644
--- a/workers/dockerfiles/Dockerfile.salmon
+++ b/workers/dockerfiles/Dockerfile.salmon
@@ -24,36 +24,34 @@ ENV SALMON_VERSION=0.13.1
 # On version 0.13.1 salmon was being extracted to a folder with an all
 # lowercase name the options `-C` and `--strip-components` allow us to specify
 #the name for the resulting file.
-RUN wget -q "https://github.com/COMBINE-lab/salmon/releases/download/\
-v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz" && \
-    mkdir "Salmon-${SALMON_VERSION}_linux_x86_64" && \
-    tar -xzf "Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz" \
-        -C "Salmon-${SALMON_VERSION}_linux_x86_64" --strip-components 1 && \
-    ln -sf "$(pwd)/Salmon-${SALMON_VERSION}_linux_x86_64/bin/salmon" \
-        /usr/local/bin/ && \
-    rm "Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz"
+RUN <<EOF
+wget -q "https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz"
+mkdir "Salmon-${SALMON_VERSION}_linux_x86_64"
+tar -xzf "Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz" -C "Salmon-${SALMON_VERSION}_linux_x86_64" --strip-components 1
+ln -sf "$(pwd)/Salmon-${SALMON_VERSION}_linux_x86_64/bin/salmon" /usr/local/bin/
+rm "Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz"
+EOF
 # End Salmon installation.
 
 ENV SRA_VERSION=2.9.1
 
 # Install SalmonTools.
-RUN git clone https://github.com/COMBINE-lab/SalmonTools.git && \
-    cd SalmonTools && \
-    git checkout 3e6654c2c10a5225498b623056993947fa688afc && \
-    cmake . -DCMAKE_INSTALL_PREFIX=/usr/local && \
-    make install && \
-    rm -rf SalmonTools && \
-    # Install sra-tools.
-    wget -q "https://ftp.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/\
-sratoolkit.${SRA_VERSION}-ubuntu64.tar.gz" && \
-    tar zxfv "sratoolkit.${SRA_VERSION}-ubuntu64.tar.gz" && \
-    cp -r "sratoolkit.${SRA_VERSION}-ubuntu64/bin/"* /usr/bin && \
-    rm "sratoolkit.${SRA_VERSION}-ubuntu64.tar.gz"
+RUN <<EOF
+git clone https://github.com/COMBINE-lab/SalmonTools.git
+cd SalmonTools
+git checkout 3e6654c2c10a5225498b623056993947fa688afc
+cmake . -DCMAKE_INSTALL_PREFIX=/usr/local
+make install
+rm -rf SalmonTools
+wget -q "https://ftp.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/sratoolkit.${SRA_VERSION}-ubuntu64.tar.gz"
+tar zxfv "sratoolkit.${SRA_VERSION}-ubuntu64.tar.gz" && \
+cp -r "sratoolkit.${SRA_VERSION}-ubuntu64/bin/"* /usr/bin && \
+rm "sratoolkit.${SRA_VERSION}-ubuntu64.tar.gz"
+EOF
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .
diff --git a/workers/dockerfiles/Dockerfile.smasher b/workers/dockerfiles/Dockerfile.smasher
index 077e6e110..a89196d42 100644
--- a/workers/dockerfiles/Dockerfile.smasher
+++ b/workers/dockerfiles/Dockerfile.smasher
@@ -16,8 +16,7 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Get the latest version from the dist directory.
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .
diff --git a/workers/dockerfiles/Dockerfile.transcriptome b/workers/dockerfiles/Dockerfile.transcriptome
index a27cc15aa..766065870 100644
--- a/workers/dockerfiles/Dockerfile.transcriptome
+++ b/workers/dockerfiles/Dockerfile.transcriptome
@@ -16,26 +16,25 @@ ENV SALMON_VERSION=0.13.1
 
 COPY workers/data_refinery_workers/processors/requirements.txt .
 # Salmon can extract to a different directory than the name of the tar file.
-RUN wget -q "https://github.com/COMBINE-lab/salmon/releases/download/\
-v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz" && \
-    tar -xzf "Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz" && \
-    cp "$(tar -tzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz | \
-        head -1 | cut -f1 -d '/')/bin/salmon" /usr/local/bin && \
-    cp "$(tar -tzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz | \
-        head -1 | cut -f1 -d '/')/lib/"* /usr/local/lib/ && \
-    rm -r Salmon*
+RUN <<EOF
+wget -q "https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz"
+tar -xzf "Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz"
+cp "$(tar -tzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz | head -1 | cut -f1 -d '/')/bin/salmon" /usr/local/bin
+cp "$(tar -tzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz | head -1 | cut -f1 -d '/')/lib/"* /usr/local/lib/
+rm -r Salmon*
+EOF
 # End Salmon installation.
 
 COPY workers/data_refinery_workers/processors/requirements.txt .
-RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt && \
-    # It's annoying that this can only be installed via git.
-    git clone https://github.com/deweylab/RSEM.git && \
-    cd RSEM && make install && \
-    rm -rf RSEM
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir -r requirements.txt
+git clone https://github.com/deweylab/RSEM.git
+cd RSEM && make install
+rm -rf RSEM
+EOF
 
 COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir \
-        common/$(ls common -1 | sort --version-sort | tail -1)
+RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
 
 COPY .boto .boto
 COPY workers/ .