From b8602a93081975e3226aa4e60d87cba7580bd01d Mon Sep 17 00:00:00 2001
From: Arkadii Yakovets <ark@ccdatalab.org>
Date: Thu, 2 Nov 2023 15:11:47 -0700
Subject: [PATCH] Optimize docker image build process

  - Run affymetrix/agilent tests in parallel
  - Set file permissions to 644 while copying
  - Set directory permissions to 755
  - Exclude unnecessary files vie dockerignore
---
 .dockerignore                                | 19 +++++++------
 .github/workflows/config.yml                 |  2 +-
 api/dockerfiles/Dockerfile.api               |  3 +-
 api/dockerfiles/Dockerfile.api_base          | 19 +++++++++----
 common/dockerfiles/Dockerfile.base           | 10 +++++--
 common/dockerfiles/Dockerfile.common_tests   | 13 ++++++---
 common/dockerfiles/Dockerfile.migrations     |  9 ++++--
 foreman/dockerfiles/Dockerfile.foreman       | 20 +++++++++----
 workers/dockerfiles/Dockerfile.affymetrix    | 28 +++++++++++-------
 workers/dockerfiles/Dockerfile.compendia     | 28 +++++++++++-------
 workers/dockerfiles/Dockerfile.downloaders   | 26 +++++++++++------
 workers/dockerfiles/Dockerfile.illumina      | 30 ++++++++++++--------
 workers/dockerfiles/Dockerfile.no_op         | 26 ++++++++++-------
 workers/dockerfiles/Dockerfile.salmon        | 22 ++++++++------
 workers/dockerfiles/Dockerfile.smasher       | 26 ++++++++++-------
 workers/dockerfiles/Dockerfile.transcriptome | 20 ++++++++-----
 16 files changed, 191 insertions(+), 110 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index c2205b57e..41934125e 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,15 +1,16 @@
-.git
-*/batch-job-specs
-*/test_volume
-*/volume
+**/.git
+**/__pycache__
+**/*.pyc
+**/batch-job-templates
+**/dockerfiles
+**/environments
+**/test_volume
+**/volume
+**/volumes_postgres
 config/externally_supplied_metadata/metasra/*.tab
 config/externally_supplied_metadata/metasra/metasra_keywords.json
 config/externally_supplied_metadata/metasra/metasra_translated.json
 config/externally_supplied_metadata/metasra/SRAmetadb.sqlite
 dr_env
 env/
-infrastructure/
-terraform/
-test_volume
-volume
-volumes_postgres/
+infrastructure
diff --git a/.github/workflows/config.yml b/.github/workflows/config.yml
index bd9fe259c..7b5d96fde 100644
--- a/.github/workflows/config.yml
+++ b/.github/workflows/config.yml
@@ -85,7 +85,7 @@ jobs:
     env:
       IMAGES: migrations affymetrix
     needs:
-      - test_affymetrix
+      - test_base
     runs-on: ubuntu-latest-m
     steps:
       - uses: actions/checkout@v3
diff --git a/api/dockerfiles/Dockerfile.api b/api/dockerfiles/Dockerfile.api
index 292d1149a..3fd03b67b 100644
--- a/api/dockerfiles/Dockerfile.api
+++ b/api/dockerfiles/Dockerfile.api
@@ -8,8 +8,9 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 RUN <<EOF
 pip install --ignore-installed --no-cache-dir uwsgi
 chmod +x /home/user/collect_and_run_uwsgi.sh
-mkdir -p /tmp/www/static
+mkdir -m 755 -p /tmp/www/static
 chown user /tmp/www/static
+rm -rf /root/.cache/*
 EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/api/dockerfiles/Dockerfile.api_base b/api/dockerfiles/Dockerfile.api_base
index 3503db769..53764b60c 100644
--- a/api/dockerfiles/Dockerfile.api_base
+++ b/api/dockerfiles/Dockerfile.api_base
@@ -15,17 +15,24 @@ EOF
 
 WORKDIR /home/user
 
-COPY api/requirements.txt .
+COPY --chmod=644 api/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/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
+
+COPY --chmod=644 api/ .
+COPY --chmod=644 config/ config/
+COPY --chmod=644 setup.cfg .
 
-COPY api/ .
-COPY config/ config/
-COPY setup.cfg .
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+EOF
 
 ENTRYPOINT []
diff --git a/common/dockerfiles/Dockerfile.base b/common/dockerfiles/Dockerfile.base
index ad21342e6..f2f4c5633 100644
--- a/common/dockerfiles/Dockerfile.base
+++ b/common/dockerfiles/Dockerfile.base
@@ -65,9 +65,13 @@ 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
+COPY --chmod=644 config/ config/
+COPY --chmod=644 setup.cfg .
 
-COPY config/ config/
-COPY setup.cfg .
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+EOF
+
+ENV R_LIBS=/usr/local/lib/R/site-library
 
 ENTRYPOINT []
diff --git a/common/dockerfiles/Dockerfile.common_tests b/common/dockerfiles/Dockerfile.common_tests
index 3d5cf4f05..228b27871 100644
--- a/common/dockerfiles/Dockerfile.common_tests
+++ b/common/dockerfiles/Dockerfile.common_tests
@@ -7,14 +7,19 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY common/R/dependencies/common_tests/renv.lock .
-COPY common/R/renv_load.R renv_load_common_tests.R
+COPY --chmod=644 common/R/dependencies/common_tests/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_common_tests.R
 RUN Rscript renv_load_common_tests.R
 
-COPY common/requirements.txt .
+COPY --chmod=644 common/requirements.txt .
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
-COPY common/ .
+COPY --chmod=644 common/ .
+
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/common/dockerfiles/Dockerfile.migrations b/common/dockerfiles/Dockerfile.migrations
index 516ce642b..9edaa2bd1 100644
--- a/common/dockerfiles/Dockerfile.migrations
+++ b/common/dockerfiles/Dockerfile.migrations
@@ -7,10 +7,15 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY common/requirements.txt .
+COPY --chmod=644 common/requirements.txt .
 RUN pip install --ignore-installed --no-cache-dir -r requirements.txt
 
-COPY common/ .
+COPY --chmod=644 common/ .
+
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/foreman/dockerfiles/Dockerfile.foreman b/foreman/dockerfiles/Dockerfile.foreman
index baf0cad7d..357d24e91 100644
--- a/foreman/dockerfiles/Dockerfile.foreman
+++ b/foreman/dockerfiles/Dockerfile.foreman
@@ -7,9 +7,9 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY foreman/requirements.txt .
+COPY --chmod=644 foreman/requirements.txt .
 RUN <<EOF
-mkdir -p data/microarray
+mkdir -m 755 -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
@@ -17,11 +17,19 @@ 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/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
+
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 foreman/ .
 
-COPY .boto .boto
-COPY foreman/ .
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/workers/dockerfiles/Dockerfile.affymetrix b/workers/dockerfiles/Dockerfile.affymetrix
index 478d377a5..e2a07e37a 100644
--- a/workers/dockerfiles/Dockerfile.affymetrix
+++ b/workers/dockerfiles/Dockerfile.affymetrix
@@ -7,24 +7,30 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY workers/R/dependencies/affymetrix/renv.lock .
-COPY common/R/renv_load.R renv_load_affymetrix.R
+COPY --chmod=644 workers/R/dependencies/affymetrix/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_affymetrix.R
 RUN Rscript renv_load_affymetrix.R
 
-COPY workers/R/dependencies/affymetrix/install_ensg_pkgs.R .
+COPY --chmod=644 workers/R/dependencies/affymetrix/install_ensg_pkgs.R .
 RUN Rscript install_ensg_pkgs.R
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 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/$(ls common -1 | sort --version-sort | tail -1)
-
-COPY .boto .boto
-COPY workers/ .
-
-RUN rm -rf /root/.cache/*
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
+
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
+
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/workers/dockerfiles/Dockerfile.compendia b/workers/dockerfiles/Dockerfile.compendia
index e4f3cf557..fe6eface1 100644
--- a/workers/dockerfiles/Dockerfile.compendia
+++ b/workers/dockerfiles/Dockerfile.compendia
@@ -68,14 +68,14 @@ WORKDIR /home/user
 
 ENV R_LIBS=/usr/local/lib/R/site-library
 
-COPY workers/R/dependencies/compendia/renv.lock .
-COPY common/R/renv_load.R renv_load_compendia.R
+COPY --chmod=644 workers/R/dependencies/compendia/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_compendia.R
 RUN Rscript renv_load_compendia.R
 
-COPY workers/data_refinery_workers/requirements/compendia.txt requirements.txt
+COPY --chmod=644 workers/data_refinery_workers/requirements/compendia.txt requirements.txt
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
-COPY workers/data_refinery_workers/processors/requirements.txt requirements.txt
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt requirements.txt
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Install phantomjs.
@@ -87,15 +87,21 @@ 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/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
-COPY .boto .boto
-COPY config/ config/
-COPY setup.cfg .
-COPY workers/ .
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 config/ config/
+COPY --chmod=644 setup.cfg .
+COPY --chmod=644 workers/ .
 
-RUN rm -rf /root/.cache/*
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ARG SYSTEM_VERSION
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.downloaders b/workers/dockerfiles/Dockerfile.downloaders
index cdedb2b60..af7030e4e 100644
--- a/workers/dockerfiles/Dockerfile.downloaders
+++ b/workers/dockerfiles/Dockerfile.downloaders
@@ -7,11 +7,11 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY workers/R/dependencies/downloaders/renv.lock .
-COPY common/R/renv_load.R renv_load_downloaders.R
+COPY --chmod=644 workers/R/dependencies/downloaders/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_downloaders.R
 RUN Rscript renv_load_downloaders.R
 
-COPY workers/data_refinery_workers/downloaders/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/downloaders/requirements.txt .
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Install Aspera.
@@ -23,8 +23,10 @@ EOF
 
 USER user
 
+ENV GNUPG_PATH=/home/user/.gnupg
+
 RUN <<EOF
-mkdir -m 700 /home/user/.gnupg
+mkdir -m 700 ${GNUPG_PATH}
 # Disable IPv6 to avoid "Cannot assign requested address" error.
 echo "disable-ipv6" >> /home/user/.gnupg/dirmngr.conf
 . /home/user/rvm/scripts/rvm
@@ -34,13 +36,19 @@ 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/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
-COPY .boto .boto
-COPY workers/ .
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
 
-RUN rm -rf /root/.cache/*
+RUN <<EOF
+rm -rf /root/.cache/*
+find /home/user -path ${GNUPG_PATH} -prune -type d ! -perm 755 -exec chmod 755 {} \;
+EOF
 
 ENV PATH="$PATH:/home/user/.aspera/sdk"
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
diff --git a/workers/dockerfiles/Dockerfile.illumina b/workers/dockerfiles/Dockerfile.illumina
index 54ac5539a..50885503c 100644
--- a/workers/dockerfiles/Dockerfile.illumina
+++ b/workers/dockerfiles/Dockerfile.illumina
@@ -7,23 +7,29 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY workers/R/dependencies/illumina/renv.lock .
-COPY common/R/renv_load.R renv_load_illumina.R
+COPY --chmod=644 workers/R/dependencies/illumina/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_illumina.R
 RUN Rscript renv_load_illumina.R
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 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/$(ls common -1 | sort --version-sort | tail -1)
-
-COPY .boto .boto
-COPY workers/ .
-COPY workers/data_refinery_workers/processors/detect_database.R .
-COPY workers/illumina_probe_maps/ probe_maps/
-
-RUN rm -rf /root/.cache/*
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
+
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
+COPY --chmod=644 workers/data_refinery_workers/processors/detect_database.R .
+COPY --chmod=644 workers/illumina_probe_maps/ probe_maps/
+
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/workers/dockerfiles/Dockerfile.no_op b/workers/dockerfiles/Dockerfile.no_op
index 3fd393005..3f3bb35c4 100644
--- a/workers/dockerfiles/Dockerfile.no_op
+++ b/workers/dockerfiles/Dockerfile.no_op
@@ -7,17 +7,17 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY workers/R/dependencies/no_op/renv.lock .
-COPY common/R/renv_load.R renv_load_no_op.R
+COPY --chmod=644 workers/R/dependencies/no_op/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_no_op.R
 RUN Rscript renv_load_no_op.R
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Noop-specific.
-RUN mkdir -p gene_indexes
+RUN mkdir -m 755 -p gene_indexes
 WORKDIR /home/user/gene_indexes
-ENV ID_REFINERY_URL=https://zenodo.org/record/1410647/files/all_1536267482.zip
+ENV ID_REFINERY_URL=https://zenodo.org/records/1410647/files/all_1536267482.zip
 RUN <<EOF
 echo $ID_REFINERY_URL > /etc/identifier_refinery_url
 wget $ID_REFINERY_URL
@@ -29,13 +29,19 @@ EOF
 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/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
-COPY .boto .boto
-COPY workers/ .
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
 
-RUN rm -rf /root/.cache/*
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/workers/dockerfiles/Dockerfile.salmon b/workers/dockerfiles/Dockerfile.salmon
index 4a103f8b2..7e4ab49f5 100644
--- a/workers/dockerfiles/Dockerfile.salmon
+++ b/workers/dockerfiles/Dockerfile.salmon
@@ -7,11 +7,11 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY workers/R/dependencies/salmon/renv.lock .
-COPY common/R/renv_load.R renv_load_salmon.R
+COPY --chmod=644 workers/R/dependencies/salmon/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_salmon.R
 RUN Rscript renv_load_salmon.R
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 
 # Install Salmon
@@ -50,13 +50,19 @@ 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/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
-COPY .boto .boto
-COPY workers/ .
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
 
-RUN rm -rf /root/.cache/*
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/workers/dockerfiles/Dockerfile.smasher b/workers/dockerfiles/Dockerfile.smasher
index a89196d42..939c3d6f1 100644
--- a/workers/dockerfiles/Dockerfile.smasher
+++ b/workers/dockerfiles/Dockerfile.smasher
@@ -7,21 +7,27 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /home/user
 
-COPY workers/R/dependencies/smasher/renv.lock .
-COPY common/R/renv_load.R renv_load_smasher.R
+COPY --chmod=644 workers/R/dependencies/smasher/renv.lock .
+COPY --chmod=644 common/R/renv_load.R renv_load_smasher.R
 RUN Rscript renv_load_smasher.R
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 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/$(ls common -1 | sort --version-sort | tail -1)
-
-COPY .boto .boto
-COPY workers/ .
-
-RUN rm -rf /root/.cache/*
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
+
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
+
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION
 
diff --git a/workers/dockerfiles/Dockerfile.transcriptome b/workers/dockerfiles/Dockerfile.transcriptome
index 766065870..89c32a6b4 100644
--- a/workers/dockerfiles/Dockerfile.transcriptome
+++ b/workers/dockerfiles/Dockerfile.transcriptome
@@ -14,7 +14,7 @@ WORKDIR /home/user
 # all samples from incomplete experiments must have salmon run on them again.
 ENV SALMON_VERSION=0.13.1
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 # Salmon can extract to a different directory than the name of the tar file.
 RUN <<EOF
 wget -q "https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz"
@@ -25,7 +25,7 @@ rm -r Salmon*
 EOF
 # End Salmon installation.
 
-COPY workers/data_refinery_workers/processors/requirements.txt .
+COPY --chmod=644 workers/data_refinery_workers/processors/requirements.txt .
 RUN <<EOF
 pip3 install --ignore-installed --no-cache-dir -r requirements.txt
 git clone https://github.com/deweylab/RSEM.git
@@ -33,13 +33,19 @@ cd RSEM && make install
 rm -rf RSEM
 EOF
 
-COPY common/dist/data-refinery-common-* common/
-RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+COPY --chmod=644 common/dist/data-refinery-common-* common/
+RUN <<EOF
+pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
+rm -r common
+EOF
 
-COPY .boto .boto
-COPY workers/ .
+COPY --chmod=644 .boto .boto
+COPY --chmod=644 workers/ .
 
-RUN rm -rf /root/.cache/*
+RUN <<EOF
+find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
+rm -rf /root/.cache/*
+EOF
 
 ENV SYSTEM_VERSION=$SYSTEM_VERSION