changeset 2:386bf3c10c46 draft default tip

Uploaded
author ketan
date Tue, 15 Oct 2013 16:22:17 -0400
parents 7aa6ee21028c
children
files README.txt
diffstat 1 files changed, 42 insertions(+), 0 deletions(-) [+]
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+A simple Hello World Swift tool to run with Galaxy.
+
+To set up with your Galaxy environment follow the steps below:
+0. Prerequisite: Sun/Oracle java. Should work with IBM java but not tested rigorously.
+
+1. Download and install Swift where Galaxy server is running. From a command prompt the following wget will pull the latest release:
+
+wget http://www.ci.uchicago.edu/swift/packages/swift-0.94.1.tar.gz
+
+Do untar at a suitable location:
+
+tar zxf swift-0.94.1.tar.gz
+
+Put the bin dir on system PATH:
+
+export PATH=$PATH:/location/to/swift-0.94.1/bin
+
+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).
+
+Make sure Swift is available from a command prompt:
+
+which swift
+swift -version
+
+2. untar and copy the swift-galaxy.tgz to the tools directory of your Galaxy location:
+
+tar zxf swift-galaxy.tgz
+
+cp -r swift-galaxy /location/of/galaxy-server/tools/
+
+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:
+
+<section name="swift-hello" id="swift-hello">
+  <tool file="swift-galaxy/helloswift.xml" />
+</section>
+
+4. Restart the Galaxy server. The swift-galaxy tool should be available in the tool box of Galaxy GUI.
+
+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.
+
+Please note that the Cluster option is not implemented in this example.
+