docker-min-env/000755 000765 000024 00000000000 13335275067 016256 5ustar00etiennedumoulinstaff000000 000000 docker-min-env/bin/000755 000765 000024 00000000000 13335275130 017015 5ustar00etiennedumoulinstaff000000 000000 docker-min-env/Dockerfile000644 000765 000024 00000000350 13335275067 020246 0ustar00etiennedumoulinstaff000000 000000 FROM ubuntu:18.04 RUN apt-get update && apt-get install -y locales && rm -rf /var/lib/apt/lists/* \ && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 ENV LANG en_US.utf8 ADD . /code WORKDIR /code docker-min-env/bin/install-omerocli-ubuntu.sh000644 000765 000024 00000003133 13335275010 024143 0ustar00etiennedumoulinstaff000000 000000 #!/bin/bash set -x OMERO_OPT_DIR=/opt/omero apt-get update # installed for convenience apt-get -y install unzip wget bc # install Java apt-get -y install software-properties-common add-apt-repository -y ppa:openjdk-r/ppa apt-get update apt-get -y install openjdk-8-jre # install dependencies apt-get update apt-get -y install \ unzip \ wget \ python-{pip,tables,virtualenv,yaml,jinja2} # Omero Core apt-get -y install zlib1g-dev apt-get -y install python-{pillow,numpy} # Install Ice export DEBIAN_FRONTEND=noninteractive apt-get -y install db5.3-util apt-get -y install libssl-dev libbz2-dev libmcpp-dev libdb++-dev libdb-dev apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 5E6DA83306132997 apt-add-repository "deb http://zeroc.com/download/apt/ubuntu`lsb_release -rs` stable main" apt-get update apt-get -y install zeroc-ice-all-runtime zeroc-ice-all-dev pip install "zeroc-ice>3.5,<3.7" # install Postgres apt-get -y install apt-transport-https add-apt-repository -y "deb https://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main 9.6" wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - apt-get update apt-get -y install postgresql-9.6 # Create an omero user adduser -disabled-password -q --gecos "" phenomic mkdir -p "$OMERO_OPT_DIR" cd $OMERO_OPT_DIR SERVER=https://downloads.openmicroscopy.org/latest/omero5/server-ice36.zip wget $SERVER -O OMERO.server-ice36.zip unzip -q OMERO.server* ln -s OMERO.server-*/ OMERO.server chown -R phenomic $PWD echo "export PYTHON_PATH=/opt/omero/server/OMERO.server/lib/python:$PYTHON_PATH" >> /home/phenomic/.bashrc docker-min-env/bin/start-docker.sh000755 000765 000024 00000001564 13335275010 021761 0ustar00etiennedumoulinstaff000000 000000 #!/bin/bash SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )" export NETWORK=phen_docker_network export POSTGRES_PASSWORD=postgres export OMERO_ROOTPASS=omero-root-password docker network create $NETWORK docker stop postgres docker stop omero-server docker stop phenomic docker rm postgres docker rm omero-server docker rm phenomic docker run -d --name postgres --net $NETWORK -e POSTGRES_PASSWORD=$POSTGRES_PASSWORD postgres docker run -d --name omero-server --net $NETWORK \ -e CONFIG_omero_db_user=postgres \ -e CONFIG_omero_db_pass=$POSTGRES_PASSWORD \ -e CONFIG_omero_db_name=postgres \ -e CONFIG_omero_db_host=postgres \ -e ROOTPASS=$OMERO_ROOTPASS \ -p 4063:4063 -p 4064:4064 \ openmicroscopy/omero-server docker build $SCRIPT_DIR/.. -t phenomic-platform docker run -td --name phenomic --net $NETWORK phenomic-platform