Commit 7e23e2cc authored by Ben Taylor's avatar Ben Taylor
Browse files

Reformat README to markdown

parent 44c13396
......@@ -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)
......@@ -15,7 +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/
......@@ -23,12 +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.
......@@ -37,7 +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
......
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