Commit 2d86d6f8 authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

Merge pull request #215 from sanger-pathogens/BT5_travis

Add TravisCI Support, change README to markdown
parents 4ea2cb1d f1e26e13
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)" ]
...@@ -72,7 +72,7 @@ manual : ...@@ -72,7 +72,7 @@ manual :
CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print` 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 : dist :
rm -rf artemis_compiled.tar.gz tar_build rm -rf artemis_compiled.tar.gz tar_build
...@@ -112,24 +112,24 @@ artemis.jar : $(CLASSES) ...@@ -112,24 +112,24 @@ artemis.jar : $(CLASSES)
done; \ done; \
fi; \ fi; \
cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \ 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 '*.java' -print | xargs rm -f
find jar_build -name '.svn' -print | xargs rm -rf find jar_build -name '.svn' -print | xargs rm -rf
cd jar_build; \ cd jar_build; \
rm -rf META-INF/MANIFEST.MF; \ rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \ 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; \ 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; \ 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; \ 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; \ 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; \ 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; \ 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; \ artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
rm -f etc/log4j.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 uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
clean : clean :
......
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 Artemis is a free genome browser and annotation tool that allows visualisation
of sequence features, next generation data and the results of analyses within 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 ...@@ -13,7 +15,7 @@ difference between genomes and to explore conservation of synteny, in the contex
of the entire sequences and their annotation. of the entire sequences and their annotation.
DOCUMENTATION # DOCUMENTATION
The Artemis user manual is at: The Artemis user manual is at:
http://www.sanger.ac.uk/resources/software/artemis/ http://www.sanger.ac.uk/resources/software/artemis/
...@@ -21,12 +23,12 @@ The Artemis user manual is at: ...@@ -21,12 +23,12 @@ The Artemis user manual is at:
The ACT user manual is at: The ACT user manual is at:
http://www.sanger.ac.uk/resources/software/act/ http://www.sanger.ac.uk/resources/software/act/
INSTALLATION # INSTALLATION
The installation instructions are included in the user manual. The installation instructions are included in the user manual.
DISTRIBUTION # DISTRIBUTION
Artemis may be freely distributed under the terms of the GNU Public License, 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. 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: ...@@ -35,7 +37,7 @@ For information on how to get Artemis see this web page:
http://www.sanger.ac.uk/resources/software/artemis/ http://www.sanger.ac.uk/resources/software/artemis/
COPYRIGHT COPYRIGHT
Copyright (C) 1998-2013 Genome Research Limited Copyright (C) 1998-2013 Genome Research Limited
......
#!/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
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