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1 A simple Hello World Swift tool to run with Galaxy.
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2
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3 To set up with your Galaxy environment follow the steps below:
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4 0. Prerequisite: Sun/Oracle java. Should work with IBM java but not tested rigorously.
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5
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6 1. Download and install Swift where Galaxy server is running. From a command prompt the following wget will pull the latest release:
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7
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8 wget http://www.ci.uchicago.edu/swift/packages/swift-0.94.1.tar.gz
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9
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10 Do untar at a suitable location:
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11
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12 tar zxf swift-0.94.1.tar.gz
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13
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14 Put the bin dir on system PATH:
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15
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16 export PATH=$PATH:/location/to/swift-0.94.1/bin
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17
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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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19
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20 Make sure Swift is available from a command prompt:
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21
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22 which swift
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23 swift -version
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24
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25 2. untar and copy the swift-galaxy.tgz to the tools directory of your Galaxy location:
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26
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27 tar zxf swift-galaxy.tgz
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28
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29 cp -r swift-galaxy /location/of/galaxy-server/tools/
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30
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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:
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32
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33 <section name="swift-hello" id="swift-hello">
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34 <tool file="swift-galaxy/helloswift.xml" />
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35 </section>
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36
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37 4. Restart the Galaxy server. The swift-galaxy tool should be available in the tool box of Galaxy GUI.
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38
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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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40
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41 Please note that the Cluster option is not implemented in this example.
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42
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