--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 09 12:20:31 2015 -0400
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fiji" version="20141125">
+        <install version="1.0">
+            <actions_group>
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-linux64-20141125.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-macosx-20141125.dmg</action>
+                    <action type="shell_command">
+                    	hdiutil attach fiji-macosx-20141125.dmg &amp;&amp;
+                    	cp -R /Volumes/Fiji/Fiji.app/ $INSTALL_DIR &amp;&amp;
+                    	hdiutil detach /Volumes/Fiji
+                    </action>
+                </actions>
+                <actions>
+                    <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-nojre-20141125.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable name="FIJI_JAR_DIR" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                    <environment_variable name="FIJI_PLUGIN_DIR" action="set_to">$INSTALL_DIR/plugins</environment_variable>
+                    <environment_variable name="FIJI_OSX_JAVA3D_DIR" action="set_to">$INSTALL_DIR/java/macosx-java3d/Home/lib/ext</environment_variable>
+                    <environment_variable name="FIJI_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Contents/MacOS</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+            <![CDATA[
+                Fiji is an image processing package.  It can be described as a "batteries-included" distribution of
+                ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure.
+                Fiji compares to ImageJ as Ubuntu compares to Linux.  The main focus of Fiji is to assist research in
+                life sciences.
+                
+                ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
+                It runs, either as an online applet or as a downloadable application, on any computer with a
+                Java 1.4 or later virtual machine.
+                
+                It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read
+                many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a
+                series of images that share a single window. It is multithreaded, so time-consuming operations such
+                as image file reading can be performed in parallel with other operations.
+                
+                See http://rsb.info.nih.gov/ij/docs/intro.html
+                
+                NOTE: If you are planning to run ImageJ2 from the command line (unusual if using Galaxy) on Yosemite,
+                then this version of fiji must be patched - see 
+                http://fiji.sc/Frequently_Asked_Questions#How_do_I_run_ImageJ_on_Yosemite.3F
+            ]]>
+        </readme>
+    </package>
+</tool_dependency>