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garrettjstevensgarrettjstevens
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Merge branch 'develop'
2 parents da8e4ac + 1b2b9db commit c8accac

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‎.devcontainer/Dockerfile

-32
This file was deleted.

‎.devcontainer/devcontainer.json

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
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// https://github.com/microsoft/vscode-dev-containers/tree/v0.224.2/containers/java-8
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
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{
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"name": "Java 8",
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"build": {
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"dockerfile": "Dockerfile",
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"args": {
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// Use the VARIANT arg to pick a Debian OS version: buster, bullseye
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// Use bullseye when running on local arm64/Apple Silicon.
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"VARIANT": "bullseye",
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// Options
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"INSTALL_MAVEN": "false",
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"INSTALL_GRADLE": "true",
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"NODE_VERSION": "12"
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"name": "Apollo",
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// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
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"image": "mcr.microsoft.com/devcontainers/base:jammy",
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"features": {
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"ghcr.io/devcontainers-extra/features/gradle-sdkman:2": {
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"version": "2.11",
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"jdkVersion": "8",
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"jdkDistro": "tem"
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},
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"ghcr.io/devcontainers-extra/features/grails-sdkman:2": {
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"version": "2.5.5",
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"jdkVersion": "8",
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"jdkDistro": "tem"
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},
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"ghcr.io/devcontainers-extra/features/groovy-sdkman:2": {
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"version": "latest",
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"jdkVersion": "8",
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"jdkDistro": "tem"
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},
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"ghcr.io/devcontainers/features/node:1": {
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"version": "12"
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}
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},
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"java.jdt.java.ls.home": "/docker-java-home",
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"java.import.gradle.java.home": "/usr/local/sdkman/candidates/java/current",
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"java.configuration.runtimes": [{
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"default": true,
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"name": "JavaSE-1.8",
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"path": "/usr/local/sdkman/candidates/java/current"
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}]
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},
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}
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": [
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"vscjava.vscode-java-pack"
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],
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// Features to add to the dev container. More info: https://containers.dev/features.
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// "features": {},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Use 'postCreateCommand' to run commands after the container is created.
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"postCreateCommand": "pipx install apollo",
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// "postCreateCommand": "uname -a",
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// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
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"remoteUser": "vscode",
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"features": {
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"git": "os-provided",
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"python": "os-provided"
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}
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// Configure tool-specific properties.
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// "customizations": {},
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// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "root"
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}

‎.github/workflows/python-apollo.yml

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@@ -9,7 +9,7 @@ jobs:
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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python-version: [3.8.7]
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python-version: [3.9]
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steps:
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- name: Checkout Apollo
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uses: actions/checkout@v2
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run: |
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pwd
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cd python-apollo
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pip install -U pip setuptools nose apollo
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- uses: actions/cache@v2
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pip install "setuptools==68.2.2" nose apollo
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- uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/local-apollo2-arrow.yml
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python setup.py nosetests
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- uses: actions/cache@v2
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- uses: actions/cache@v4
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with:
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path: |
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~/.gradle/caches
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restore-keys: |
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${{ runner.os }}-gradle-
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- name: Cache local Maven repository
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: ~/.m2/repository
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key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}

‎ChangeLog.md

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## 2.8.0
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Bug Fixes
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- Security fixes
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Infrastructure Changes
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- Upgrade to [JBrowse 1.16.12](https://github.com/GMOD/jbrowse/releases/tag/1.16.12-release)
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## 2.7.0
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Features

‎Dockerfile

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# Apollo2.X
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FROM ubuntu:20.04
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MAINTAINER Nathan Dunn GH @nathandunn
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ENV DEBIAN_FRONTEND noninteractive
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ENV DEBIAN_FRONTEND=noninteractive
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# where bin directories are
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ENV CATALINA_HOME /usr/share/tomcat9
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ENV CATALINA_HOME=/usr/share/tomcat9
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# where webapps are deployed
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ENV CATALINA_BASE /var/lib/tomcat9
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ENV CONTEXT_PATH ROOT
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ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64
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RUN apt-get -qq update --fix-missing && \
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apt-get --no-install-recommends -y install \
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git locales locales-all build-essential libpq-dev wget python3-pip \
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lsb-release gnupg2 wget xmlstarlet netcat libpng-dev postgresql-common \
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zlib1g-dev libexpat1-dev curl ssl-cert zip unzip openjdk-8-jdk-headless
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RUN sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list' && \
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wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
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RUN apt-get -qq update --fix-missing && \
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apt-get --no-install-recommends -y install \
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postgresql-9.6 postgresql-client-9.6 tomcat9 && \
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apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /apollo/
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RUN curl -sL https://deb.nodesource.com/setup_12.x | bash -
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RUN apt-get -qq update --fix-missing && \
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apt-get --no-install-recommends -y install nodejs
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RUN curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" -o /usr/local/bin/blat && \
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chmod +x /usr/local/bin/blat && \
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curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" -o /usr/local/bin/faToTwoBit && \
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chmod +x /usr/local/bin/faToTwoBit && \
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wget --quiet https://github.com/galaxy-genome-annotation/chado-schema-builder/releases/download/1.31-jenkins26/chado-1.31.sql.gz -O /chado.sql.gz && \
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gunzip /chado.sql.gz
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ENV CATALINA_BASE=/var/lib/tomcat9
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ENV CONTEXT_PATH=ROOT
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ENV JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
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RUN <<EOF
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apt-get -qq update --fix-missing
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apt-get --no-install-recommends -y install git locales locales-all \
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build-essential libpq-dev wget python3-pip lsb-release gnupg2 wget xmlstarlet \
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netcat libpng-dev postgresql-common zlib1g-dev libexpat1-dev curl ssl-cert zip \
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unzip openjdk-8-jdk-headless
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sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list'
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wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
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apt-get -qq update --fix-missing
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apt-get --no-install-recommends -y install postgresql-9.6 \
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postgresql-client-9.6 tomcat9
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apt-get autoremove -y
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /apollo/
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curl -sL https://deb.nodesource.com/setup_12.x | bash -
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apt-get -qq update --fix-missing
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apt-get --no-install-recommends -y install nodejs
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curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" -o /usr/local/bin/blat
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chmod +x /usr/local/bin/blat
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curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" -o /usr/local/bin/faToTwoBit
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chmod +x /usr/local/bin/faToTwoBit
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wget --quiet https://github.com/galaxy-genome-annotation/chado-schema-builder/releases/download/1.31-jenkins26/chado-1.31.sql.gz -O /chado.sql.gz
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gunzip /chado.sql.gz
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#NOTE, we had problems with the build the archive-file coming in from github so using a clone instead
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RUN npm i -g yarn && useradd -ms /bin/bash -d /apollo apollo
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npm i -g yarn
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useradd -ms /bin/bash -d /apollo apollo
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EOF
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COPY client /apollo/client
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COPY gradlew /apollo
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COPY grails-app /apollo/grails-app
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COPY docker-files/build.sh /bin/build.sh
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ADD docker-files/docker-apollo-config.groovy /apollo/apollo-config.groovy
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RUN chown -R apollo:apollo /apollo
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RUN <<EOF
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mkdir /var/lib/postgresql
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mkdir /data
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chown -R apollo:apollo /apollo
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chown -R apollo:apollo ${CATALINA_BASE}
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chown -R apollo:apollo ${CATALINA_HOME}
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chown -R apollo:apollo /var/run/postgresql
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chown -R apollo:apollo /var/lib/postgresql
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chown -R apollo:apollo /etc/tomcat9
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chown -R apollo:apollo /var/log/tomcat9
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chown -R apollo:apollo /var/cache/tomcat9
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chown -R apollo:apollo /data
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EOF
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# install python libraries
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# fix for pip install decode error
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# RUN locale-gen en_US.UTF-8
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ENV LC_CTYPE en_US.UTF-8
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ENV LC_ALL en_US.UTF-8
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ENV LANG en_US.UTF-8
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ENV LC_CTYPE=en_US.UTF-8
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ENV LC_ALL=en_US.UTF-8
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ENV LANG=en_US.UTF-8
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ENV LANGUAGE=en_US.UTF-8
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RUN pip3 install setuptools
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RUN pip3 install wheel
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RUN pip3 install nose apollo==4.2.10
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RUN <<EOF
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pip3 install setuptools
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pip3 install wheel
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pip3 install nose apollo==4.2.10
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EOF
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# install grails
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USER apollo
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RUN curl -s get.sdkman.io | bash && \
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/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5" && \
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/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install gradle 3.2.1"
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RUN <<EOF
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curl -s https://get.sdkman.io | bash
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/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5"
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/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install gradle 3.2.1"
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RUN /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && /bin/bash /bin/build.sh"
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/bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && /bin/bash /bin/build.sh"
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USER root
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# remove from webapps and copy it into a staging directory
87-
RUN rm -rf ${CATALINA_BASE}/webapps/* && \
88-
cp /apollo/apollo*.war ${CATALINA_BASE}/apollo.war
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rm -rf ${CATALINA_BASE}/webapps/*
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cp /apollo/apollo*.war ${CATALINA_BASE}/apollo.war
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EOF
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ADD docker-files/createenv.sh /createenv.sh
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ADD docker-files/launch.sh /launch.sh
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CMD "/launch.sh"
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CMD ["/launch.sh"]

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