Mercurial > repos > iuc > package_fiji_20141125

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author iuc
date Fri, 26 Jun 2015 12:48:05 -0400
parents 7121a1ea4839
children
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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="20141125">
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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://fiji.sc/downloads/Life-Line/fiji-linux64-20141125.tar.gz</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://fiji.sc/downloads/Life-Line/fiji-macosx-20141125.dmg</action>
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15 <action type="shell_command">
1
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16 hdiutil attach fiji-macosx-20141125.dmg &amp;&amp;
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17 cp -R /Volumes/Fiji/Fiji.app/ $INSTALL_DIR &amp;&amp;
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18 hdiutil detach /Volumes/Fiji
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19 ## The ImageJ launcher contained in this version of Fiji will not
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20 ## run on Yosemite due to some operating system change. The following
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21 ## block will download the fixed ImageJ launcher for Yosemite. This is
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22 ## kind of a stop-gap measure for this recipe only (notice the use of
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23 ## wget, which is not an approved best practice). This problem affects
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24 ## only those running Yosemite, and will be eliminated in the next
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25 ## stable version of Fiji when it is released.
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26 if [[ `sw_vers -productVersion | tr -d '.'` -ge 1010 ]]; then
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27 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;
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28 xattr -c imagej-launcher &amp;&amp;
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29 chmod +x imagej-launcher &amp;&amp;
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30 mv imagej-launcher $INSTALL_DIR/Contents/MacOS/ImageJ-macosx
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31 fi
0
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32 </action>
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33 </actions>
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34 <actions>
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35 <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-nojre-20141125.zip</action>
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36 <action type="move_directory_files">
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37 <source_directory>.</source_directory>
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38 <destination_directory>$INSTALL_DIR</destination_directory>
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39 </action>
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40 </actions>
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41 <action type="set_environment">
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42 <environment_variable name="FIJI_JAR_DIR" action="set_to">$INSTALL_DIR/jars</environment_variable>
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43 <environment_variable name="FIJI_PLUGIN_DIR" action="set_to">$INSTALL_DIR/plugins</environment_variable>
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44 <environment_variable name="FIJI_OSX_JAVA3D_DIR" action="set_to">$INSTALL_DIR/java/macosx-java3d/Home/lib/ext</environment_variable>
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45 <environment_variable name="FIJI_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
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46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Contents/MacOS</environment_variable>
2
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47 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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48
0
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49 </action>
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50 </actions_group>
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51 </install>
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52 <readme>
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53 <![CDATA[
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54 Fiji is an image processing package. It can be described as a "batteries-included" distribution of
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55 ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure.
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56 Fiji compares to ImageJ as Ubuntu compares to Linux. The main focus of Fiji is to assist research in
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57 life sciences.
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58
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59 ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
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60 It runs, either as an online applet or as a downloadable application, on any computer with a
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61 Java 1.4 or later virtual machine.
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62
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63 It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read
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64 many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a
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65 series of images that share a single window. It is multithreaded, so time-consuming operations such
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66 as image file reading can be performed in parallel with other operations.
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67
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68 See http://rsb.info.nih.gov/ij/docs/intro.html
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69
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70 NOTE: If you are planning to run ImageJ2 from the command line (unusual if using Galaxy) on Yosemite,
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71 then this version of fiji must be patched - see
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72 http://fiji.sc/Frequently_Asked_Questions#How_do_I_run_ImageJ_on_Yosemite.3F
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73 ]]>
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74 </readme>
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75 </package>
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76 </tool_dependency>