startup script

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8931 ee4ac58c-ac51-4696-9907-e4b3aa274f04

dnaplot

+#!/bin/sh -
+
+# This script will start the Artemis circular plot on a UNIX system.  
+
+# resolve links - $0 may be a link
+PRG=$0
+progname=`basename $0`
+
+ARTEMIS_HOME=`dirname "$PRG"`/.
+
+CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.1-407.jdbc2ee.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH
+
+# j2ssh jars
+CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/j2ssh/commons-logging.jar:$ARTEMIS_HOME/lib/j2ssh/j2ssh-core.jar:$ARTEMIS_HOME/lib/j2ssh/
+
+# iBatis jars
+CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.0.677.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2_beta1.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar
+export CLASSPATH
+
+
+ARTEMIS_PROPERTIES="-Dartemis.environment=UNIX"
+
+# Allow URLs to work from behind firewalls
+if [ "$http_proxy" = "" ]
+then
+  http_proxy=$HTTP_PROXY
+fi
+
+if [ "$http_proxy" = "" ]
+then
+  http_proxy=$HTTP_proxy
+fi
+
+if [ "$http_proxy" != "" ]
+then
+  ARTEMIS_PROPERTIES="$ARTEMIS_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
+fi
+
+
+# "-mx500m" sets the maximum amount of memory that Artemis can use.  This may
+# need to be increased when dealing with large files
+MEM="-mx500m -ms20m"
+
+if [ "$JVM_FLAGS" = "" ]
+then
+    FLAGS="$MEM -noverify"
+else
+    FLAGS="$MEM -noverify $JVM_FLAGS"
+fi
+
+
+FLAGS=$FAST_FLAG$FLAGS
+
+if [ "$JAVA_VM" = "" ]
+then
+    if [ "$DEBUG" = yes ]
+    then
+        JAVA=java_g
+    else
+        JAVA=java
+    fi
+else
+    JAVA=$JAVA_VM
+fi
+
+PLATTMP=`uname`
+if [ "$PLATTMP" = "Darwin" ]
+then
+  FLAGS="$FLAGS -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Circular Plot"
+fi
+
+$JAVA $MEM uk.ac.sanger.artemis.circular.DNADraw $*