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comparison tool_dependencies.xml @ 0:e9cc903e877c draft default tip

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author iuc
date Thu, 21 Apr 2016 10:29:04 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="fiji" version="20151222">
4 <install version="1.0">
5 <actions_group>
6 <actions os="linux" architecture="x86_64">
7 <action type="download_by_url">http://downloads.imagej.net/fiji/Life-Line/fiji-linux64-20151222.zip</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <actions os="darwin" architecture="x86_64">
14 <action type="download_by_url">http://downloads.imagej.net/fiji/Life-Line/fiji-macosx-20151222.dmg</action>
15 <action type="shell_command">
16 hdiutil attach fiji-macosx-20151222.dmg &amp;&amp;
17 cp -R /Volumes/Fiji/Fiji.app/ $INSTALL_DIR &amp;&amp;
18 hdiutil detach /Volumes/Fiji
19 </action>
20 </actions>
21 <actions>
22 <action type="download_by_url">http://downloads.imagej.net/fiji/Life-Line/fiji-nojre-20151222.zip</action>
23 <action type="move_directory_files">
24 <source_directory>.</source_directory>
25 <destination_directory>$INSTALL_DIR</destination_directory>
26 </action>
27 </actions>
28 <action type="set_environment">
29 <environment_variable name="FIJI_JAR_DIR" action="set_to">$INSTALL_DIR/jars</environment_variable>
30 <environment_variable name="FIJI_PLUGIN_DIR" action="set_to">$INSTALL_DIR/plugins</environment_variable>
31 <environment_variable name="FIJI_OSX_JAVA3D_DIR" action="set_to">$INSTALL_DIR/java/macosx-java3d/Home/lib/ext</environment_variable>
32 <environment_variable name="FIJI_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
33 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Contents/MacOS</environment_variable>
34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
35 </action>
36 </actions_group>
37 </install>
38 <readme>
39 <![CDATA[
40 Fiji is an image processing package. It can be described as a "batteries-included" distribution of
41 ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure.
42 Fiji compares to ImageJ as Ubuntu compares to Linux. The main focus of Fiji is to assist research in
43 life sciences.
44
45 ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
46 It runs, either as an online applet or as a downloadable application, on any computer with a
47 Java 1.4 or later virtual machine.
48
49 It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read
50 many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a
51 series of images that share a single window. It is multithreaded, so time-consuming operations such
52 as image file reading can be performed in parallel with other operations.
53
54 See http://rsb.info.nih.gov/ij/docs/intro.html
55
56 NOTE: If you are planning to run ImageJ2 from the command line (unusual if using Galaxy) on Yosemite,
57 then this version of fiji must be patched - see
58 http://fiji.sc/Frequently_Asked_Questions#How_do_I_run_ImageJ_on_Yosemite.3F
59 ]]>
60 </readme>
61 </package>
62 </tool_dependency>