Merge pull request #294 from sanger-pathogens/docker_branch

Add a docker file, build and documentation updates. Fix for issue 293.

.gitignore

@@ -9,3 +9,4 @@ maven.properties
 .evosuite
 maven-archiver
 .dribble.*
+.Dockerfile*

.travis.yml

@@ -6,7 +6,7 @@ env:
 sudo: true
 matrix:
   include:
-    - jdk: oraclejdk9
+    - jdk: oraclejdk12
       env: 
        - TEST_EXCLUDES="**/*_ESTest*"
     - jdk: openjdk9
@@ -19,10 +19,11 @@ cache:
   directories:
   - "${HOME}/dependencies"
   - "${HOME}/.m2"
+services:
+  - xvfb
 before_install:
   - "export CASHER_TIME_OUT=300"
   - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
   - "source install_dependencies.sh"
   - mvn validate
 install:
@@ -32,4 +33,4 @@ script:
       cd test;
       ln -s $(pwd)/../etc/log4j.properties .;
       ./RunTravisTests.sh -e "$TEST_EXCLUDES" | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];
-    fi
+    fi

Dockerfile

@@ -0,0 +1,83 @@
+##############################################################
+# Experimental Docker file for the Artemis software suite.
+#
+# Please see usage documentation at Docker Hub:
+#
+# https://hub.docker.com/r/sangerpathogens/artemis
+#
+##############################################################
+FROM ubuntu:18.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+LABEL maintainer="path-help@sanger.ac.uk"
+
+# Build and environment configuration
+ARG ARTEMIS_BUILD_DIR=/artemis-build
+ARG INSTALL_DIR=/opt/artemis
+ARG BLAST_INSTALL_DIR=/usr/local/ncbi/blast/
+ARG BROWSER_INSTALL_DIR=/usr/local/firefox
+ARG ARTEMIS_WORKDIR=/artemis
+ENV JAVA_OPTS="-Dsun.jnu.encoding=UTF-8 -Dfile.encoding=UTF-8"
+ENV LANG="en_US.UTF-8"
+ENV LANGUAGE="en_US.UTF-8"
+ENV LC_ALL="en_US.UTF-8"
+ENV LC_COLLATE="en_US.UTF-8"
+ENV LC_CTYPE="en_US.UTF-8"
+
+# Mount points
+RUN mkdir -p $ARTEMIS_WORKDIR && chmod 777 $ARTEMIS_WORKDIR
+
+# Install main dependencies
+RUN apt-get update --quiet --assume-yes
+RUN apt-get upgrade --quiet --assume-yes
+RUN apt-get install --quiet --assume-yes locales openjdk-11-jdk libxtst6 libxrender1 libxext6 libexpat1 fonts-dejavu-core fontconfig-config libfontconfig1 libfreetype6 libpng16-16 curl wget maven ant
+RUN update-alternatives --config java
+RUN update-alternatives --config javac
+
+RUN echo "Java version installed: `java -version`"
+
+# Set locale
+RUN echo en_US.UTF-8 UTF-8 >> /etc/locale.gen
+RUN locale-gen en_US.UTF-8
+
+# Build and install Artemis
+# No tests are run currently as some of them pop up windows and hence require X
+RUN mkdir -p $INSTALL_DIR
+RUN mkdir -p $ARTEMIS_BUILD_DIR
+COPY . $ARTEMIS_BUILD_DIR
+RUN cd $ARTEMIS_BUILD_DIR && mvn validate && mvn -Djarsigner.skip=true -Dskip.tests=true package -P release
+RUN tar xvf $ARTEMIS_BUILD_DIR/target/release-artifacts/unix-release/artemis-unix-release-*.tar.gz --strip-components=1 -C ${INSTALL_DIR}
+RUN rm -rf $ARTEMIS_BUILD_DIR && rm -rf ~/.m2
+
+# Install Blast+
+RUN mkdir -p $BLAST_INSTALL_DIR
+RUN curl --fail -L ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz | tar xzf - --strip-components=1 -C $BLAST_INSTALL_DIR
+
+# Install Firefox for use with pfam etc (use firejail for increased security)
+RUN apt-get install --quiet --assume-yes libgtk-3-0 libdbus-glib-1-2 libxt6 firejail
+RUN mkdir -p $BROWSER_INSTALL_DIR
+RUN wget -O firefox.tar.bz2 "https://download.mozilla.org/?product=firefox-latest-ssl&os=linux64&lang=en-GB" && \
+    tar xvf /firefox.tar.bz2 && \
+    rm -f /firefox.tar.bz2 && \
+    mv /firefox /usr/local/
+
+RUN echo "firejail --private --dns=8.8.8.8 --dns=8.8.4.4 $BROWSER_INSTALL_DIR/firefox -no-remote "'"$@"' > /usr/bin/firefox && chmod 555 /usr/bin/firefox
+
+# Cleanup
+RUN apt-get autoremove
+RUN apt-get clean
+
+# Environment
+ENV PATH=$INSTALL_DIR:$INSTALL_DIR/dist:$INSTALL_DIR/etc:$BLAST_INSTALL_DIR/bin:$PATH
+ENV CLASSPATH=$INSTALL_DIR:$INSTALL_DIR/dist:$INSTALL_DIR/etc:${CLASSPATH}
+ENV HOME=$ARTEMIS_WORKDIR
+WORKDIR $ARTEMIS_WORKDIR
+
+# Define default command.
+CMD   echo 'Usage:  docker run -d -e DISPLAY="<your display name>:0" -v <your user home directory>:/home/artuser -v <your data folder>:/artemis' && \
+      echo '          --user $(id -u):$(id -g) -e ARTEMIS_JVM_FLAGS="-Duser.home=/home/artuser -Djava.io.tmpdir=/tmp" --tmpfs /tmp' && \
+      echo '          --rm artemis <program name [art|act|bamview|dnaplotter]> [program arguments]' && \
+      echo && \
+      echo 'For help, please go to http://sanger-pathogens.github.io/Artemis/'
+

README.md

@@ -3,15 +3,18 @@ The Artemis Software is a set of software tools for genome browsing and annotati
 
 [![Build Status](https://travis-ci.org/sanger-pathogens/Artemis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Artemis)  
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Artemis/blob/master/LICENSE)  
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/artemis/README.html)   
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/artemis/README.html)  
+![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/sangerpathogens/artemis)  
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2F16.10.944-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/16.10.944)  
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtr703-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btr703)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn529-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn529)   
 [![status](https://img.shields.io/badge/BIB-10.1093%2Fbib%2F4.2.124-brightgreen.svg)](https://doi.org/10.1093/bib/4.2.124)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbti553-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/bti553)   
 [![status](https://img.shields.io/badge/BIB-10.1093%2Fbib%2Fbbr073-brightgreen.svg)](https://doi.org/10.1093/bib/bbr073)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtq010-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btq010)   
-[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn578-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn578)   
+[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn578-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn578)  
+
+![GitHub Releases (by Release)](https://img.shields.io/github/downloads/sanger-pathogens/artemis/v18.0.2/total)
 
 ## Contents
   * [Introduction](#introduction)
@@ -41,7 +44,7 @@ For further information and details on how to download the Artemis software, ple
 
 ## Prerequisites
 
-Java 9+ must be installed. Ideally Java 11.
+Java version 9 or later must be installed. Ideally Java 11 should be used. The easiest way to install a non-commercial open source Java version is from [AdoptOpenJDK](https://adoptopenjdk.net/releases.html) - just select the OpenJDK 11 and Hotspot options for the relevant platform. See the [GitHub pages and manuals](#documentation) for further options. A Java installation is not required if installing via Bioconda or Docker.
 
 ## Installation
 
@@ -78,7 +81,7 @@ mvn -Dhttps.proxyHost=myproxyhost -Dhttps.proxyPort=myproxyport -DproxySet=true
 ```
 This will build the application jars and place them in target/jars and win-jars folders. The win-jars jars have the etc folder files bundled in, for Windows.
 
-## Building Release artifacts
+## Building Release Artifacts
 To build .zip or .gz installables with unsigned jars, use the following command:
 ```
 mvn -Djarsigner.skip=true clean package -P release
@@ -154,6 +157,9 @@ For more information on how to download Artemis, please see the [Artemis GitHub
 
 ## Documentation
 
+Artemis GitHub pages:
+  http://sanger-pathogens.github.io/Artemis/
+
 The Artemis user manual is at:
   http://sanger-pathogens.github.io/Artemis/Artemis/
 

etc/versions

@@ -1,4 +1,4 @@
-Artemis Release 18.0.2
-ACT Release 18.0.2
-DNAPlotter Release 18.0.2
-BamView 18.0.2
+Artemis Release 18.0.3
+ACT Release 18.0.3
+DNAPlotter Release 18.0.3
+BamView 18.0.3

maven-lib/README.txt

@@ -1,9 +1,9 @@
 The appbundler jar was compiled from:
 
-https://bitbucket.org/infinitekind/appbundler/overview
+https://github.com/TheInfiniteKind/appbundler/
 
 The jar is run by simply running "ant"
 
-Currently compiled in Java 10 (compatible with Java 8+). This project is a fork of the Oracle appbundler.
+Currently compiled in Java 11. This project is a fork of the Oracle appbundler.
 
-Date: 18 Oct 2018
+Date: 06 Aug 2019

pom.xml

@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>uk.ac.sanger</groupId>
 	<artifactId>artemis</artifactId>
-	<version>18.0.2</version>
+	<version>18.0.3</version>
 
 	<name>Artemis</name>
 	<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
@@ -360,7 +360,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
                 <inherited>true</inherited>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-enforcer-plugin</artifactId>
-                <version>1.3.1</version>
+                <version>1.4.1</version>
                 <executions>
                     <execution>
                         <id>enforce-maven-3</id>