[Swift-commit] r7692 - SwiftApps/swift-galaxy

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-03-11 13:44:06 -0500 (Tue, 11 Mar 2014)
New Revision: 7692

Modified:
   SwiftApps/swift-galaxy/README
Log:
swift galaxy installation instructions

Modified: SwiftApps/swift-galaxy/README
===================================================================
--- SwiftApps/swift-galaxy/README	2014-03-11 18:34:47 UTC (rev 7691)
+++ SwiftApps/swift-galaxy/README	2014-03-11 18:44:06 UTC (rev 7692)
@@ -4,39 +4,68 @@
 Introduction
 -------------
 
+The Swift-Galaxy integration project aims to build tools which can be used to
+leverage the best features of http://swift-lang.org/main[Swift] and
+http://galaxyproject.org[Galaxy] combined. We start with building a generic
+Galaxy tool, called `foreach` which allows user to compose Galaxy workflows
+such that each computation stage in the workflow is executed by Swift. User can
+compose Galaxy tool and pick up arbitrary executables and dataset to run the
+executable over.
+
 How To
 ------
 
-Step 1. Symlink the swift directory in the current directory from galaxy's top level directory. For example, if Galaxy top level directory is galaxy-dist and swift directory is /home/ketan/SwiftApps/swift-galaxy/swift,
+Step 1. Symlink the swift directory in the current directory from galaxy's top
+level directory. For example, if Galaxy top level directory is galaxy-dist and
+swift directory is /home/ketan/SwiftApps/swift-galaxy/swift:
 
 ----
 cd galaxy-dist
 ln -s /home/ketan/SwiftApps/swift-galaxy/swift swift
 ----
 
-Step 2. Add the tool definitions of the tools contained in this Swift to Galaxy's tool_conf.xml. This can be done by copying the text in <section>...</section> from the tool_conf.xml in swift-galaxy directory and paste it to the tool_conf.xml of the Galaxy directory.
+Step 2. Add the tool definitions of the tools contained in this Swift to
+Galaxy's tool_conf.xml. This can be done by copying the text in
+`<section>...</section>` from the tool_conf.xml in swift-galaxy directory and
+paste it to the tool_conf.xml of the Galaxy directory.
 
-Step 3. (Re)start Galaxy. You should see the tools in a toolset titled Swift.
+Step 3. (Re)start Galaxy.
 
+----
+sh run.sh
+----
 
+In the Galaxy Web GUI, you should see the tools in a toolset titled Swift.
+
 An example
 ----------
 
 A simple Hello World Swift tool to run with Galaxy.
 
 To set up with your Galaxy environment follow the steps below:
-Prerequisite: Sun/Oracle java. Should work with IBM java but not tested.
+Prerequisite: Sun/Oracle java. Should work with IBM java but not tested. To test your java version:
 
-Step 1. Download and install Swift where Galaxy server is running. From a command prompt the following wget will pull the latest release:
+----
+java -version
+----
 
+Typical output is:
+
 ----
-wget http://swiftlang.org/packages/swift-0.94.2-RC2.tar.gz
+java version "1.7.0_17"
+Java(TM) SE Runtime Environment (build 1.7.0_17-b02)
+Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode)
 ----
 
-Step 2. Create a swift-tool directory and copy the Swift tool skeleton files in this directory
+Step 1. Download and install Swift where Galaxy server is running. From a
+command prompt the following wget will pull the latest release from
+http://swift-lang.org/downloads/index.php[here].
 
+Step 2. SVN checkout the swift-galaxy directory and copy the Swift tool directory to Galaxy's tools directory:
+
 ----
-cp swift/swift-skeleton* /location/of/galaxy-server/tools/
+svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/swift-galaxy
+cp -r swift-galaxy/swift /location/of/galaxy-server/tools/
 ----
 
 Step 3. Edit the tool_conf.xml file present at the top-level of galaxy directory tree to add the following lines between the <toolbox> and </toolbox> xml tags: