Mercurial > repos > iuc > package_fiji_20141125

annotate tool_dependencies.xml @ 1:7121a1ea4839 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
author iuc
date Wed, 10 Jun 2015 09:08:22 -0400
parents 2957c52b8fe0
children 9dbe89105a25
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
2 <tool_dependency>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
3 <package name="fiji" version="20141125">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
4 <install version="1.0">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
5 <actions_group>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
6 <actions os="linux" architecture="x86_64">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
7 <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-linux64-20141125.tar.gz</action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
8 <action type="move_directory_files">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
9 <source_directory>.</source_directory>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
10 <destination_directory>$INSTALL_DIR</destination_directory>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
11 </action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
12 </actions>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
13 <actions os="darwin" architecture="x86_64">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
14 <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-macosx-20141125.dmg</action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
15 <action type="shell_command">
1
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
16 hdiutil attach fiji-macosx-20141125.dmg &amp;&amp;
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
17 cp -R /Volumes/Fiji/Fiji.app/ $INSTALL_DIR &amp;&amp;
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
18 hdiutil detach /Volumes/Fiji
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
19 ## The ImageJ launcher contained in this version of Fiji will not
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
20 ## run on Yosemite due to some operating system change. The following
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
21 ## block will download the fixed ImageJ launcher for Yosemite. This is
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
22 ## kind of a stop-gap measure for this recipe only (notice the use of
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
23 ## wget, which is not an approved best practice). This problem affects
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
24 ## only those running Yosemite, and will be eliminated in the next
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
25 ## stable version of Fiji when it is released.
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
26 if [[ `sw_vers -productVersion | tr -d '.'` -ge 1010 ]]; then
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
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;
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
28 xattr -c imagej-launcher &amp;&amp;
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
29 chmod +x imagej-launcher &amp;&amp;
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
30 mv imagej-launcher $INSTALL_DIR/Contents/MacOS/ImageJ-macosx
7121a1ea4839 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 55da61c256450682512bc4cbc26471eb77b88bed
iuc
parents: 0
diff changeset
31 fi
0
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
32 </action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
33 </actions>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
34 <actions>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
35 <action type="download_by_url">http://fiji.sc/downloads/Life-Line/fiji-nojre-20141125.zip</action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
36 <action type="move_directory_files">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
37 <source_directory>.</source_directory>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
38 <destination_directory>$INSTALL_DIR</destination_directory>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
39 </action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
40 </actions>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
41 <action type="set_environment">
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
42 <environment_variable name="FIJI_JAR_DIR" action="set_to">$INSTALL_DIR/jars</environment_variable>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
43 <environment_variable name="FIJI_PLUGIN_DIR" action="set_to">$INSTALL_DIR/plugins</environment_variable>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
44 <environment_variable name="FIJI_OSX_JAVA3D_DIR" action="set_to">$INSTALL_DIR/java/macosx-java3d/Home/lib/ext</environment_variable>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
45 <environment_variable name="FIJI_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Contents/MacOS</environment_variable>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
47 </action>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
48 </actions_group>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
49 </install>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
50 <readme>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
51 <![CDATA[
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
52 Fiji is an image processing package. It can be described as a "batteries-included" distribution of
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
53 ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure.
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
54 Fiji compares to ImageJ as Ubuntu compares to Linux. The main focus of Fiji is to assist research in
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
55 life sciences.
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
56
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
57 ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
58 It runs, either as an online applet or as a downloadable application, on any computer with a
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
59 Java 1.4 or later virtual machine.
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
60
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
61 It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
62 many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
63 series of images that share a single window. It is multithreaded, so time-consuming operations such
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
64 as image file reading can be performed in parallel with other operations.
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
65
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
66 See http://rsb.info.nih.gov/ij/docs/intro.html
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
67
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
68 NOTE: If you are planning to run ImageJ2 from the command line (unusual if using Galaxy) on Yosemite,
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
69 then this version of fiji must be patched - see
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
70 http://fiji.sc/Frequently_Asked_Questions#How_do_I_run_ImageJ_on_Yosemite.3F
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
71 ]]>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
72 </readme>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
73 </package>
2957c52b8fe0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_fiji_20141125 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
74 </tool_dependency>