Merge pull request #215 from sanger-pathogens/BT5_travis

Add TravisCI Support, change README to markdown

.travis.yml

+language: java
+jdk:
+  - openjdk7
+  - openjdk6
+  - oraclejdk7
+sudo: false
+env:
+  global:
+    - BUILD_CMD='make'
+matrix:
+  include:
+    - jdk: openjdk7
+      env: BUILD_CMD='ant -f build.xml'
+cache:
+  directories:
+  - "${HOME}/dependencies"
+before_install:
+  - "export CASHER_TIME_OUT=300"
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - "source install_dependencies.sh"
+install:
+  - "$BUILD_CMD"
+  - "cd test"
+  - "ln -s $(pwd)/../etc/log4j.properties ."
+script: ant -f build-test.xml test -DEMBOSS_ROOT=$EMBOSS_ROOT | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ]

Makefile

@@ -72,7 +72,7 @@ manual :
 
 CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print`
 
-OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README`
+OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README.md`
 
 dist :
 	rm -rf artemis_compiled.tar.gz tar_build
@@ -112,24 +112,24 @@ artemis.jar : $(CLASSES)
           done; \
         fi; \
 	cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
-	      ../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap .
+	      ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap .
 	find jar_build -name '*.java' -print | xargs rm -f
 	find jar_build -name '.svn' -print | xargs rm -rf
 	cd jar_build; \
 	rm -rf META-INF/MANIFEST.MF; \
 	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
-	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
 	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
         echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
-        jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
+        jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README.md etc \
                              uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
 	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
 	jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
 	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
-	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
 	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
 	rm -f etc/log4j.properties; \
-	jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README \
+	jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README.md \
 	        uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
 
 clean :

README → README.md

-INTRODUCTION
+# INTRODUCTION
+
+[![Build Status](https://travis-ci.org/sanger-pathogens/Artemis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Artemis)
 
 Artemis is a free genome browser and annotation tool that allows visualisation 
 of sequence features, next generation data and the results of analyses within 
@@ -13,7 +15,7 @@ difference between genomes and to explore conservation of synteny, in the contex
 of the entire sequences and their annotation.
 
 
-DOCUMENTATION
+# DOCUMENTATION
 
 The Artemis user manual is at:
   http://www.sanger.ac.uk/resources/software/artemis/
@@ -21,12 +23,12 @@ The Artemis user manual is at:
 The ACT user manual is at:
   http://www.sanger.ac.uk/resources/software/act/
 
-INSTALLATION
+# INSTALLATION
 
 The installation instructions are included in the user manual.
 
 
-DISTRIBUTION
+# DISTRIBUTION
 
 Artemis may be freely distributed under the terms of the GNU Public License,
 and should run on any system with a recent version of Java.  
@@ -35,7 +37,7 @@ For information on how to get Artemis see this web page:
   http://www.sanger.ac.uk/resources/software/artemis/
 
 
-COPYRIGHT
+# COPYRIGHT
 
 Copyright (C) 1998-2013  Genome Research Limited
 

install_dependencies.sh

+#!/bin/bash
+
+set -x
+set -e
+
+start_dir=$(pwd)
+
+EMBOSS_VERSION="6.6.0"
+
+EMBOSS_DOWNLOAD_URL="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EMBOSS_VERSION}.tar.gz"
+
+# Make an install location
+if [ ! -d "${HOME}/dependencies" ]; then
+  mkdir ${HOME}/dependencies
+fi
+cd ${HOME}/dependencies
+build_dir=$(pwd)
+
+# DOWNLOAD ALL THE THINGS
+download () {
+  url=$1
+  download_location=$2
+
+  if [ -e $download_location ]; then
+    echo "Skipping download of $url, $download_location already exists"
+  else
+    echo "Downloading $url to $download_location"
+    wget $url -O $download_location
+  fi
+}
+
+download $EMBOSS_DOWNLOAD_URL "${build_dir}/emboss-${EMBOSS_VERSION}.tgz"
+
+# Build all the things
+cd $build_dir
+
+## Emboss
+emboss_dir=$(pwd)/EMBOSS-${EMBOSS_VERSION}
+if [ ! -d $emboss_dir ]; then
+  tar xzf emboss-${EMBOSS_VERSION}.tgz
+fi
+cd $emboss_dir
+if [ -e "${emboss_dir}/build/bin/restrict" ]; then
+  echo "Already built Emboss; skipping build"
+else
+  mkdir build
+  ./configure --prefix ${emboss_dir}/build
+  make
+  make install
+fi
+
+export EMBOSS_ROOT=${emboss_dir}/build
+
+cd $start_dir
+
+set +x
+set +e