<?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
                        ## The ImageJ launcher contained in this version of Fiji will not
                        ## run on Yosemite due to some operating system change.  The following
                        ## block will download the fixed ImageJ launcher for Yosemite.  This is
                        ## kind of a stop-gap measure for this recipe only (notice the use of
                        ## wget, which is not an approved best practice).  This problem affects
                        ## only those running Yosemite, and will be eliminated in the next
                        ## stable version of Fiji when it is released.
                        if [[ `sw_vers -productVersion | tr -d '.'` -ge 1010 ]]; then
                            wget http://jenkins.imagej.net/job/ImageJ-launcher/label=MacOSX/lastSuccessfulBuild/artifact/target/nar/imagej-launcher-3.3.1-SNAPSHOT-x86_64-MacOSX-gcc-executable/bin/x86_64-MacOSX-gcc/imagej-launcher &amp;&amp;
                            xattr -c imagej-launcher &amp;&amp;
                            chmod +x imagej-launcher &amp;&amp;
                            mv imagej-launcher $INSTALL_DIR/Contents/MacOS/ImageJ-macosx
                        fi
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-nojre-20141125.zip</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$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">$INSTALL_DIR/Contents/MacOS</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</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>