failed in python pkg installation (todo)

EpistasisLab · Dec 3, 2020 · c8e51b3 · c8e51b3
1 parent 7ad961e
commit c8e51b3
Showing 1 changed file with 123 additions and 5 deletions.
diff --git a/docker/lab/Dockerfile b/docker/lab/Dockerfile
@@ -1,10 +1,102 @@
-FROM python:3.7.4-stretch
+FROM ubuntu:bionic
+
+#RUN apt-get update --fix-missing && apt-get install -y wget
 
 #nodejs
-RUN wget --quiet https://nodejs.org/dist/v11.14.0/node-v11.14.0-linux-x64.tar.xz -O ~/node.tar.xz && \
-    tar -xvf ~/node.tar.xz -C /opt/ && \
-    rm ~/node.tar.xz
-ENV PATH /opt/node-v11.14.0-linux-x64/bin:$PATH
+#RUN wget --quiet https://nodejs.org/dist/v11.14.0/node-v11.14.0-linux-x64.tar.xz -O ~/node.tar.xz && \
+#    tar -xvf ~/node.tar.xz -C /opt/ && \
+#    rm ~/node.tar.xz
+#ENV PATH /opt/node-v11.14.0-linux-x64/bin:$PATH
+
+RUN groupadd --gid 1000 node \
+  && useradd --uid 1000 --gid node --shell /bin/bash --create-home node
+
+ENV NODE_VERSION 12.20.0
+
+RUN ARCH= && dpkgArch="$(dpkg --print-architecture)" \
+    && case "${dpkgArch##*-}" in \
+      amd64) ARCH='x64';; \
+      ppc64el) ARCH='ppc64le';; \
+      s390x) ARCH='s390x';; \
+      arm64) ARCH='arm64';; \
+      armhf) ARCH='armv7l';; \
+      i386) ARCH='x86';; \
+      *) echo "unsupported architecture"; exit 1 ;; \
+    esac \
+    && set -ex \
+    # libatomic1 for arm
+    && apt-get update && apt-get install -y ca-certificates curl wget gnupg dirmngr xz-utils libatomic1 --no-install-recommends \
+    && rm -rf /var/lib/apt/lists/* \
+    && for key in \
+      4ED778F539E3634C779C87C6D7062848A1AB005C \
+      94AE36675C464D64BAFA68DD7434390BDBE9B9C5 \
+      1C050899334244A8AF75E53792EF661D867B9DFA \
+      71DCFD284A79C3B38668286BC97EC7A07EDE3FC1 \
+      8FCCA13FEF1D0C2E91008E09770F7A9A5AE15600 \
+      C4F0DFFF4E8C1A8236409D08E73BC641CC11F4C8 \
+      C82FA3AE1CBEDC6BE46B9360C43CEC45C17AB93C \
+      DD8F2338BAE7501E3DD5AC78C273792F7D83545D \
+      A48C2BEE680E841632CD4E44F07496B3EB3C1762 \
+      108F52B48DB57BB0CC439B2997B01419BD92F80A \
+      B9E2F5981AA6E0CD28160D9FF13993A75599653C \
+    ; do \
+      gpg --batch --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys "$key" || \
+      gpg --batch --keyserver hkp://ipv4.pool.sks-keyservers.net --recv-keys "$key" || \
+      gpg --batch --keyserver hkp://pgp.mit.edu:80 --recv-keys "$key" ; \
+    done \
+    && curl -fsSLO --compressed "https://nodejs.org/dist/v$NODE_VERSION/node-v$NODE_VERSION-linux-$ARCH.tar.xz" \
+    && curl -fsSLO --compressed "https://nodejs.org/dist/v$NODE_VERSION/SHASUMS256.txt.asc" \
+    && gpg --batch --decrypt --output SHASUMS256.txt SHASUMS256.txt.asc \
+    && grep " node-v$NODE_VERSION-linux-$ARCH.tar.xz\$" SHASUMS256.txt | sha256sum -c - \
+    && tar -xJf "node-v$NODE_VERSION-linux-$ARCH.tar.xz" -C /usr/local --strip-components=1 --no-same-owner \
+    && rm "node-v$NODE_VERSION-linux-$ARCH.tar.xz" SHASUMS256.txt.asc SHASUMS256.txt \
+    && apt-mark auto '.*' > /dev/null \
+    && find /usr/local -type f -executable -exec ldd '{}' ';' \
+      | awk '/=>/ { print $(NF-1) }' \
+      | sort -u \
+      | xargs -r dpkg-query --search \
+      | cut -d: -f1 \
+      | sort -u \
+      | xargs -r apt-mark manual \
+    && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \
+    && ln -s /usr/local/bin/node /usr/local/bin/nodejs \
+    # smoke tests
+    && node --version \
+    && npm --version
+
+ENV YARN_VERSION 1.22.5
+
+RUN set -ex \
+  && savedAptMark="$(apt-mark showmanual)" \
+  && apt-get update && apt-get install -y ca-certificates curl wget gnupg dirmngr --no-install-recommends \
+  && rm -rf /var/lib/apt/lists/* \
+  && for key in \
+    6A010C5166006599AA17F08146C2130DFD2497F5 \
+  ; do \
+    gpg --batch --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys "$key" || \
+    gpg --batch --keyserver hkp://ipv4.pool.sks-keyservers.net --recv-keys "$key" || \
+    gpg --batch --keyserver hkp://pgp.mit.edu:80 --recv-keys "$key" ; \
+  done \
+  && curl -fsSLO --compressed "https://yarnpkg.com/downloads/$YARN_VERSION/yarn-v$YARN_VERSION.tar.gz" \
+  && curl -fsSLO --compressed "https://yarnpkg.com/downloads/$YARN_VERSION/yarn-v$YARN_VERSION.tar.gz.asc" \
+  && gpg --batch --verify yarn-v$YARN_VERSION.tar.gz.asc yarn-v$YARN_VERSION.tar.gz \
+  && mkdir -p /opt \
+  && tar -xzf yarn-v$YARN_VERSION.tar.gz -C /opt/ \
+  && ln -s /opt/yarn-v$YARN_VERSION/bin/yarn /usr/local/bin/yarn \
+  && ln -s /opt/yarn-v$YARN_VERSION/bin/yarnpkg /usr/local/bin/yarnpkg \
+  && rm yarn-v$YARN_VERSION.tar.gz.asc yarn-v$YARN_VERSION.tar.gz \
+  && apt-mark auto '.*' > /dev/null \
+  && { [ -z "$savedAptMark" ] || apt-mark manual $savedAptMark > /dev/null; } \
+  && find /usr/local -type f -executable -exec ldd '{}' ';' \
+    | awk '/=>/ { print $(NF-1) }' \
+    | sort -u \
+    | xargs -r dpkg-query --search \
+    | cut -d: -f1 \
+    | sort -u \
+    | xargs -r apt-mark manual \
+  && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \
+  # smoke test
+  && yarn --version
 
 ARG docker_filepath=docker/lab/files
 
@@ -19,8 +111,34 @@ RUN apt-get update --fix-missing && apt-get install -y \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
+# ensure local python is preferred over distribution python
+ENV PATH /usr/local/bin:$PATH
+
+# http://bugs.python.org/issue19846
+# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
+ENV LANG C.UTF-8
+
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+ARG DEBIAN_FRONTEND=noninteractive
+RUN  apt-get update && apt-get install -y --no-install-recommends \
+		libbluetooth-dev \
+		tk-dev \
+		uuid-dev \
+	&& rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  wget python3-venv python3-numpy \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/list/*
+
+RUN python3 -m venv /venv
+ENV PATH=/venv/bin:$PATH
+RUN python --version
+RUN pip --version
+
 # setup python environment
 COPY ${docker_filepath}/requirements.txt /root/
+RUN pip install --no-cache-dir cython
 RUN pip install --no-cache-dir -r /root/requirements.txt
 ### bill's surprise fork
 RUN pip install --no-cache-dir git+https://github.com/lacava/surprise.git@1.0.8.3