Alpine / unified

Dockerfile

@@ -1,48 +1,16 @@
 # WebApollo
 # VERSION 2.0
-FROM tomcat:8-jre8
+FROM quay.io/gmod/docker-apollo:unified
 MAINTAINER Eric Rasche <[email protected]>, Anthony Bretaudeau <[email protected]>, Nathan Dunn <[email protected]>
-ENV DEBIAN_FRONTEND noninteractive 
-
-RUN apt-get -qq update --fix-missing && \
-	apt-get --no-install-recommends -y install \
-	git build-essential maven tomcat8 libpq-dev postgresql-common openjdk-8-jdk wget \
-	postgresql postgresql-client xmlstarlet netcat libpng12-dev \
-	zlib1g-dev libexpat1-dev ant curl ssl-cert
-
-RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -
-RUN apt-get -qq update --fix-missing && \
-	apt-get --no-install-recommends -y install nodejs && \
-	apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-RUN npm install -g bower && \
-	cp /usr/lib/jvm/java-8-openjdk-amd64/lib/tools.jar /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/tools.jar && \
-	useradd -ms /bin/bash -d /apollo apollo
-
-ENV WEBAPOLLO_VERSION 7b304aac81f7dab77165f37bf210a6b3cb1b8080
-RUN curl -L https://github.com/GMOD/Apollo/archive/${WEBAPOLLO_VERSION}.tar.gz | tar xzf - --strip-components=1 -C /apollo
-
-
-COPY build.sh /bin/build.sh
-ADD apollo-config.groovy /apollo/apollo-config.groovy
-
-RUN chown -R apollo:apollo /apollo
-USER apollo
-RUN bash /bin/build.sh
-USER root
-
-ENV CATALINA_HOME=/usr/local/tomcat/
-RUN rm -rf ${CATALINA_HOME}/webapps/* && \
-	cp /apollo/apollo*.war ${CATALINA_HOME}/apollo.war
-
-ENV CONTEXT_PATH ROOT
-
-# Download chado schema
-RUN wget --quiet https://github.com/erasche/chado-schema-builder/releases/download/1.31-jenkins97/chado-1.31.sql.gz -O /chado.sql.gz && \
-	gunzip /chado.sql.gz
-ADD user.sql /apollo/user.sql
-
-ADD launch.sh /launch.sh
-CMD "/launch.sh"
-
 
+RUN apk update && \
+	apk add bash perl make gcc perl-dev musl-dev db-dev && \
+	cd / && \
+	wget http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=109 -O JBrowse-1.12.3.zip && \
+	unzip JBrowse-1.12.3.zip && \
+	rm JBrowse-1.12.3.zip && \
+	cd JBrowse-1.12.3 && \
+	sed -i 's|bin/cpanm|bin/cpanm --no-wget|g' setup.sh && \
+	./bin/cpanm local::lib --no-wget && \
+	bash setup.sh && \
+	apk del make gcc perl-dev musl-dev db-dev

README.md

@@ -1,40 +1,39 @@
-# Apollo
 
-![Apollo Logo](https://github.com/GMOD/docker-apollo/raw/master/img/ApolloLogo_100x36.png)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.268535.svg)](https://doi.org/10.5281/zenodo.268535)
 
+# ![Apollo](img/ApolloLogo_100x36.png) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.268535.svg)](https://doi.org/10.5281/zenodo.268535) [![Docker Repository on Quay](https://quay.io/repository/gmod/docker-apollo/status "Docker Repository on Quay")](https://quay.io/repository/gmod/docker-apollo)
 
 > Apollo is a browser-based tool for visualisation and editing of sequence
 > annotations. It is designed for distributed community annotation efforts,
 > where numerous people may be working on the same sequences in geographically
 > different locations; real-time updating keeps all users in sync during the
 > editing process.
 
-## Running the Container
+## Quickstart
 
-The container is publicly available as `gmod/apollo:stable`. The recommended
-method for launching the container is via docker-compose due to a dependency on
-a postgres image.
+If you've never used docker before, first you will need to [install it](https://docs.docker.com/engine/installation/).
 
-There are a large number of environment variables that can be adjusted to suit
-your site's needs. These can be seen in the
-[apollo-config.groovy](https://github.com/GMOD/Apollo/blob/master/sample-docker-apollo-config.groovy)
-file.
+There are several flavours of Apollo images, based on your needs:
 
-## Quickstart
+Image      | Contents                       | Comments
+---------- | ------------------------------ | -------------
+`:latest`  | Apollo + Chado + JBrowse Tools | This is the easiest image to get started with. Just run `docker run -it -p 8080:8080 quay.io/gmod/docker-apollo`
+`:unified` | Apollo + Chado                 | Very similar to the `:latest` image, but does not include the JBrowse tools. Use this if you already have a JBrowse instance you wish to annotate
+`:bare`    | Apollo                         | The most lightweight image, especially for admins and people wishing to deploy Apollo in production.
+
+You can launch these images with `docker run` commands:
 
-This procedure starts tomcat in a standard virtualized environment with a PostgreSQL database with [Chado](http://gmod.org/wiki/Introduction_to_Chado).
+```console
+$ docker run -it -p 8080:8080 quay.io/gmod/docker-apollo:latest
+$ docker run -it -p 8080:8080 quay.io/gmod/docker-apollo:unified
+```
 
-- Install [docker](https://docs.docker.com/engine/installation/) for your system if not previously done.
-- `docker run -it -p 8888:8080 gmod/apollo:2.0.6` # for a tested release
-- `docker run -it -p 8888:8080 gmod/apollo:latest` # for the latest, remember to ```docker pull gmod/apollo``` to fetch newer versions
-- `docker run -it -p 8888:8080 gmod/apollo:apollo-only` # from apollo only (no postgresql)
-- `docker run -it -v /jbrowse/root/directory/:/data -p 8888:8080 gmod/apollo:latest`
-- `docker run -it -v /jbrowse/root/directory/:/data  -p 8888:8080 quay.io/gmod/docker-apollo` # built by quay.io
-- Apollo will be available at [http://localhost:8888/](http://localhost:8888/) (or 8888 if you don't configure the port)
+If you need to load data, you can mount a volume into the docker container:
 
-When you use the above mount directory ```/jbrowse/root/directory``` and your genome is in 
-```/jbrowse/root/directory/myawesomegenome``` you'll point to the directory: ```/data/myawesomegenome```.
+```console
+$ docker run -it -v /jbrowse/dir/:/data -p 8080:8080 quay.io/gmod/docker-apollo
+```
+
+When you access this data within Apollo, you should refer to `/jbrowse/dir/my-organism` as `/data/my-organism`
 
 ### Logging In
 
@@ -48,10 +47,8 @@ The default credentials in this image are:
 
 ### Loading Data
 
-Some sample data is baked into the container for you to play around with:
-
-![](./img/sample.png)
-
-### Chado
+Sample data is available within the container thanks to the JBrowse installation in this image. E.g.:
 
-Chado support is now baked into the GMOD docker container image.
+- `/JBrowse-1.12.3/sample_data/json/volvox`
+- `/JBrowse-1.12.3/sample_data/json/yeast`
+- `/JBrowse-1.12.3/sample_data/json/modencode`