[Swift-commit] r7688 - SwiftApps/swift-galaxy

Tue Mar 11 11:08:46 CDT 2014

Author: ketan
Date: 2014-03-11 11:08:46 -0500 (Tue, 11 Mar 2014)
New Revision: 7688

Added:
   SwiftApps/swift-galaxy/README
   SwiftApps/swift-galaxy/docbuild
Removed:
   SwiftApps/swift-galaxy/README.txt
Log:
galaxy foreach documentation

Copied: SwiftApps/swift-galaxy/README (from rev 7687, SwiftApps/swift-galaxy/README.txt)
===================================================================

--- SwiftApps/swift-galaxy/README	                        (rev 0)
+++ SwiftApps/swift-galaxy/README	2014-03-11 16:08:46 UTC (rev 7688)
@@ -0,0 +1,68 @@
+Swift Galaxy Integration
+=========================
+
+Introduction
+-------------
+
+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,
+
+----
+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 3. (Re)start Galaxy. 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.
+
+Step 1. Download and install Swift where Galaxy server is running. From a command prompt the following wget will pull the latest release:
+
+----
+wget http://swiftlang.org/packages/swift-0.94.2-RC2.tar.gz
+----
+
+Step 2. Create a swift-tool directory and copy the Swift tool skeleton files in this directory
+
+----
+cp swift/swift-skeleton* /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:
+
+----
+<section name="swift-galaxy" id="swift-galaxy">
+  <tool file="currdir/nameoftoolfile.xml" />
+</section>
+----
+
+Step 4. Restart the Galaxy server. The swift-galaxy tool should be available in the tool box of Galaxy GUI.
+
+Step 5. Invoke it by entering any number in the dialog box or leaving it to default.
+
+Step 6. For examples of other Galaxy-Swift tools, look into the swift directoty.
+
+Description of the Swift-Galaxy `foreach` tool 
+-----------------------------------------------
+
+There are two versions of foreach Swift tools in this implementation. The
+"numrangeforeach" tool is used to run a Swift foreach loop over a range of
+numbers for an arbitrary executable. The executable will run with the numbers
+as commandline arguments. User can add arbitrary string arguments in addition
+to the number argument to the call to executable.
+
+The second version is the "listforeach". It runs similar to the above described
+numrangeforeach except that the iteration takes place over a list of items
+provided as a file. Each item in the list is delivered to the selected
+executable as a first commandline argument.  

Deleted: SwiftApps/swift-galaxy/README.txt
===================================================================
--- SwiftApps/swift-galaxy/README.txt	2014-03-10 18:53:59 UTC (rev 7687)
+++ SwiftApps/swift-galaxy/README.txt	2014-03-11 16:08:46 UTC (rev 7688)
@@ -1,50 +0,0 @@
-=How to install Swift tools into Galaxy=
-
-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
-
-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.
-
-3. (Re)start Galaxy. You should see the tools in a toolset titled Swift.
-
-==An example of integrating a Swift tool into Galaxy==
-
-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.
-
-1. Download and install Swift where Galaxy server is running. From a command prompt the following wget will pull the latest release:
-
-wget http://swiftlang.org/packages/swift-0.94.2-RC2.tar.gz
-
-2. Create a swift-tool directory and copy the Swift tool skeleton files in this directory
-
-cp swift/swift-skeleton* /location/of/galaxy-server/tools/
-
-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:
-
-<section name="swift-galaxy" id="swift-galaxy">
-  <tool file="currdir/nameoftoolfile.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.
-
-6. For examples of other Galaxy-Swift tools, look into the swift directoty.
-
-== Description of the foreach* Swift-Galaxy tools ==
-
-There are two versions of foreach Swift tools in this implementation. The
-"numrangeforeach" tool is used to run a Swift foreach loop over a range of
-numbers for an arbitrary executable. The executable will run with the numbers
-as commandline arguments. User can add arbitrary string arguments in addition
-to the number argument to the call to executable.
-
-The second version is the "listforeach". It runs similar to the above described
-numrangeforeach except that the iteration takes place over a list of items
-provided as a file. Each item in the list is delivered to the selected
-executable as a first commandline argument.  

Added: SwiftApps/swift-galaxy/docbuild
===================================================================
--- SwiftApps/swift-galaxy/docbuild	                        (rev 0)
+++ SwiftApps/swift-galaxy/docbuild	2014-03-11 16:08:46 UTC (rev 7688)
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+if [ -z $1 ] ; then
+
+    asciidoc -a toc -a toclevels=2  -a max-width=750px  -a textwidth=80 -o /home/$(whoami)/public_html/swiftgalaxy.html README
+else
+    asciidoc -a toc -a toclevels=2  -a max-width=750px  -a textwidth=80 -o "$1" README
+fi    


Property changes on: SwiftApps/swift-galaxy/docbuild
___________________________________________________________________
Added: svn:executable
   + *


