From 210b46fce6895b45e3ca5e4948ed69fd59aae251 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 1 Jun 2021 16:53:41 -0600 Subject: [PATCH] Make Python libraries installed globally in Docker image (#2622) * Format Dockerfile * Make python libraries installed globally --- Dockerfile | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8adf3a2e2..f82518546 100644 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN apt-get -qq update --fix-missing && \ zlib1g-dev libexpat1-dev curl ssl-cert zip unzip openjdk-8-jdk-headless RUN sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list' && \ - wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - + wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - RUN apt-get -qq update --fix-missing && \ apt-get --no-install-recommends -y install \ @@ -31,11 +31,11 @@ RUN apt-get -qq update --fix-missing && \ RUN curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" -o /usr/local/bin/blat && \ - chmod +x /usr/local/bin/blat && \ - curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" -o /usr/local/bin/faToTwoBit && \ - chmod +x /usr/local/bin/faToTwoBit && \ - wget --quiet https://github.com/erasche/chado-schema-builder/releases/download/1.31-jenkins26/chado-1.31.sql.gz -O /chado.sql.gz && \ - gunzip /chado.sql.gz + chmod +x /usr/local/bin/blat && \ + curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" -o /usr/local/bin/faToTwoBit && \ + chmod +x /usr/local/bin/faToTwoBit && \ + wget --quiet https://github.com/erasche/chado-schema-builder/releases/download/1.31-jenkins26/chado-1.31.sql.gz -O /chado.sql.gz && \ + gunzip /chado.sql.gz #NOTE, we had problems with the build the archive-file coming in from github so using a clone instead RUN npm i -g yarn && useradd -ms /bin/bash -d /apollo apollo @@ -60,10 +60,9 @@ COPY docker-files/build.sh /bin/build.sh ADD docker-files/docker-apollo-config.groovy /apollo/apollo-config.groovy RUN chown -R apollo:apollo /apollo -# install grails and python libraries -USER apollo +# install python libraries -# fix for pip install decode error +# fix for pip install decode error # RUN locale-gen en_US.UTF-8 ENV LC_CTYPE en_US.UTF-8 ENV LC_ALL en_US.UTF-8 @@ -74,9 +73,12 @@ RUN pip3 install setuptools RUN pip3 install wheel RUN pip3 install nose apollo==4.2.10 +# install grails +USER apollo + RUN curl -s get.sdkman.io | bash && \ - /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5" && \ - /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install gradle 3.2.1" + /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5" && \ + /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install gradle 3.2.1" RUN /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && /bin/bash /bin/build.sh"