Mercurial > repos > ketan > swift
comparison README.txt @ 2:386bf3c10c46 draft default tip
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author | ketan |
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date | Tue, 15 Oct 2013 16:22:17 -0400 |
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1:7aa6ee21028c | 2:386bf3c10c46 |
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1 A simple Hello World Swift tool to run with Galaxy. | |
2 | |
3 To set up with your Galaxy environment follow the steps below: | |
4 0. Prerequisite: Sun/Oracle java. Should work with IBM java but not tested rigorously. | |
5 | |
6 1. Download and install Swift where Galaxy server is running. From a command prompt the following wget will pull the latest release: | |
7 | |
8 wget http://www.ci.uchicago.edu/swift/packages/swift-0.94.1.tar.gz | |
9 | |
10 Do untar at a suitable location: | |
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12 tar zxf swift-0.94.1.tar.gz | |
13 | |
14 Put the bin dir on system PATH: | |
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16 export PATH=$PATH:/location/to/swift-0.94.1/bin | |
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18 Edit above line to match the location of Swift and add it to your environment file (.bashrc, .bash_profile or the corresponding ones for other shells). | |
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20 Make sure Swift is available from a command prompt: | |
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22 which swift | |
23 swift -version | |
24 | |
25 2. untar and copy the swift-galaxy.tgz to the tools directory of your Galaxy location: | |
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27 tar zxf swift-galaxy.tgz | |
28 | |
29 cp -r swift-galaxy /location/of/galaxy-server/tools/ | |
30 | |
31 3. Edit the tool_conf.xml file present at the top-level of galaxy-server directory tree to add the following lines between the <toolbox> and </toolbox> xml tags: | |
32 | |
33 <section name="swift-hello" id="swift-hello"> | |
34 <tool file="swift-galaxy/helloswift.xml" /> | |
35 </section> | |
36 | |
37 4. Restart the Galaxy server. The swift-galaxy tool should be available in the tool box of Galaxy GUI. | |
38 | |
39 5. Invoke it by entering any number in the dialog box or leaving it to default. A message "Hello World!" will be written to output files as many times and the files should be available for browsing from Galaxy GUI. | |
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41 Please note that the Cluster option is not implemented in this example. | |
42 |