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Fix difference
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@arkid15r
arkid15r committed Nov 2, 2023
1 parent 3b503f8 commit 4c972fa
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Showing 14 changed files with 73 additions and 34 deletions.
3 changes: 2 additions & 1 deletion api/dockerfiles/Dockerfile.api
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Expand Up @@ -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
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19 changes: 13 additions & 6 deletions api/dockerfiles/Dockerfile.api_base
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Expand Up @@ -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 []
8 changes: 6 additions & 2 deletions common/dockerfiles/Dockerfile.base
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Expand Up @@ -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 .

RUN <<EOF
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
EOF

ENV R_LIBS=/usr/local/lib/R/site-library

ENTRYPOINT []
6 changes: 3 additions & 3 deletions common/dockerfiles/Dockerfile.common_tests
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Expand Up @@ -16,13 +16,13 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt

COPY --chmod=644 common/ .

ENV SYSTEM_VERSION=$SYSTEM_VERSION

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION

USER user

ENTRYPOINT []
6 changes: 3 additions & 3 deletions common/dockerfiles/Dockerfile.migrations
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Expand Up @@ -12,13 +12,13 @@ RUN pip install --ignore-installed --no-cache-dir -r requirements.txt

COPY --chmod=644 common/ .

ENV SYSTEM_VERSION=$SYSTEM_VERSION

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION

USER user

ENTRYPOINT []
11 changes: 7 additions & 4 deletions foreman/dockerfiles/Dockerfile.foreman
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Expand Up @@ -18,18 +18,21 @@ EOF

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 foreman/ .

ENV SYSTEM_VERSION=$SYSTEM_VERSION

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION

USER user

ENTRYPOINT []
7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.affymetrix
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Expand Up @@ -19,14 +19,17 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 workers/ .

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION
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7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.compendia
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Expand Up @@ -88,16 +88,19 @@ EOF

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 config/ config/
COPY --chmod=644 setup.cfg .
COPY --chmod=644 workers/ .

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ARG SYSTEM_VERSION
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5 changes: 4 additions & 1 deletion workers/dockerfiles/Dockerfile.downloaders
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Expand Up @@ -37,7 +37,10 @@ USER root

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 workers/ .
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7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.illumina
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Expand Up @@ -16,16 +16,19 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(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
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION
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7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.no_op
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Expand Up @@ -30,14 +30,17 @@ WORKDIR /home/user

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 workers/ .

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION
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7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.salmon
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Expand Up @@ -51,14 +51,17 @@ EOF

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 workers/ .

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION
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7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.smasher
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Expand Up @@ -16,14 +16,17 @@ RUN pip3 install --ignore-installed --no-cache-dir -r requirements.txt

# Get the latest version from the dist directory.
COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 workers/ .

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION
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7 changes: 5 additions & 2 deletions workers/dockerfiles/Dockerfile.transcriptome
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Expand Up @@ -34,14 +34,17 @@ rm -rf RSEM
EOF

COPY --chmod=644 common/dist/data-refinery-common-* common/
RUN pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
RUN <<EOF
pip3 install --ignore-installed --no-cache-dir common/$(ls common -1 | sort --version-sort | tail -1)
rm -r common
EOF

COPY --chmod=644 .boto .boto
COPY --chmod=644 workers/ .

RUN <<EOF
rm -rf /root/.cache/*
find /home/user -type d ! -perm 755 -exec chmod 755 {} \;
rm -rf /root/.cache/*
EOF

ENV SYSTEM_VERSION=$SYSTEM_VERSION
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