diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000000000000000000000000000000000000..065180db8370c77ec1d437f356d7c9747ecf0e97
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,26 @@
+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)" ]
diff --git a/Makefile b/Makefile
index 5d72710cbad59dcc60475dd0dc170c1de7f28c86..9b33c29459ff5c15bd96ce5f8c1e6a3127a2e518 100644
--- a/Makefile
+++ b/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 :
diff --git a/README b/README.md
similarity index 90%
rename from README
rename to README.md
index 510968837cbe1843842e5d84208f39e6f5b7ddfb..5c4d9bb034cafb3659ae07d89514bc5946c8ca48 100644
--- a/README
+++ b/README.md
@@ -1,4 +1,6 @@
-INTRODUCTION
+# INTRODUCTION
+
+[](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
+#Â COPYRIGHT
Copyright (C) 1998-2013 Genome Research Limited
diff --git a/install_dependencies.sh b/install_dependencies.sh
new file mode 100644
index 0000000000000000000000000000000000000000..2e6eb18c1b6663dc3695a30013520e7ed35853f7
--- /dev/null
+++ b/install_dependencies.sh
@@ -0,0 +1,57 @@
+#!/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