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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="fiji" version="20151222">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions os="linux" architecture="x86_64">
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7 <action type="download_by_url">http://downloads.imagej.net/fiji/Life-Line/fiji-linux64-20151222.zip</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 </actions>
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13 <actions os="darwin" architecture="x86_64">
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14 <action type="download_by_url">http://downloads.imagej.net/fiji/Life-Line/fiji-macosx-20151222.dmg</action>
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15 <action type="shell_command">
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16 hdiutil attach fiji-macosx-20151222.dmg &&
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17 cp -R /Volumes/Fiji/Fiji.app/ $INSTALL_DIR &&
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18 hdiutil detach /Volumes/Fiji
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19 </action>
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20 </actions>
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21 <actions>
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22 <action type="download_by_url">http://downloads.imagej.net/fiji/Life-Line/fiji-nojre-20151222.zip</action>
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23 <action type="move_directory_files">
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24 <source_directory>.</source_directory>
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25 <destination_directory>$INSTALL_DIR</destination_directory>
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26 </action>
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27 </actions>
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28 <action type="set_environment">
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29 <environment_variable name="FIJI_JAR_DIR" action="set_to">$INSTALL_DIR/jars</environment_variable>
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30 <environment_variable name="FIJI_PLUGIN_DIR" action="set_to">$INSTALL_DIR/plugins</environment_variable>
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31 <environment_variable name="FIJI_OSX_JAVA3D_DIR" action="set_to">$INSTALL_DIR/java/macosx-java3d/Home/lib/ext</environment_variable>
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32 <environment_variable name="FIJI_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
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33 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Contents/MacOS</environment_variable>
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34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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35 </action>
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36 </actions_group>
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37 </install>
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38 <readme>
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39 <![CDATA[
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40 Fiji is an image processing package. It can be described as a "batteries-included" distribution of
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41 ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure.
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42 Fiji compares to ImageJ as Ubuntu compares to Linux. The main focus of Fiji is to assist research in
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43 life sciences.
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44
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45 ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
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46 It runs, either as an online applet or as a downloadable application, on any computer with a
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47 Java 1.4 or later virtual machine.
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48
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49 It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read
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50 many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a
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51 series of images that share a single window. It is multithreaded, so time-consuming operations such
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52 as image file reading can be performed in parallel with other operations.
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53
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54 See http://rsb.info.nih.gov/ij/docs/intro.html
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55
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56 NOTE: If you are planning to run ImageJ2 from the command line (unusual if using Galaxy) on Yosemite,
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57 then this version of fiji must be patched - see
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58 http://fiji.sc/Frequently_Asked_Questions#How_do_I_run_ImageJ_on_Yosemite.3F
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59 ]]>
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60 </readme>
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61 </package>
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62 </tool_dependency>
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