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 :
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 :
......
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
......
#!/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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