[Swift-commit] r7513 - in SwiftApps/swift-galaxy: . swift

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-01-25 20:30:32 -0600 (Sat, 25 Jan 2014)
New Revision: 7513

Added:
   SwiftApps/swift-galaxy/README.txt
Removed:
   SwiftApps/swift-galaxy/README
Modified:
   SwiftApps/swift-galaxy/swift/genericswift.xml
Log:
new README

Deleted: SwiftApps/swift-galaxy/README
===================================================================
--- SwiftApps/swift-galaxy/README	2014-01-26 01:32:26 UTC (rev 7512)
+++ SwiftApps/swift-galaxy/README	2014-01-26 02:30:32 UTC (rev 7513)
@@ -1,7 +0,0 @@
-=How to install this into Galaxy=
-
-=Notes=
-
-1. Untar Illinois.tgz before running powergrid application
-2. The csvs in the lungsearch application are not complete, they contain just the first 50 lines
-

Added: SwiftApps/swift-galaxy/README.txt
===================================================================
--- SwiftApps/swift-galaxy/README.txt	                        (rev 0)
+++ SwiftApps/swift-galaxy/README.txt	2014-01-26 02:30:32 UTC (rev 7513)
@@ -0,0 +1,51 @@
+=How to install this into Galaxy=
+
+=Notes=
+
+1. Untar Illinois.tgz before running powergrid application
+2. The csvs in the lungsearch application are not complete, they contain just the first 50 lines
+
+==An example==
+
+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.
+

Modified: SwiftApps/swift-galaxy/swift/genericswift.xml
===================================================================
--- SwiftApps/swift-galaxy/swift/genericswift.xml	2014-01-26 01:32:26 UTC (rev 7512)
+++ SwiftApps/swift-galaxy/swift/genericswift.xml	2014-01-26 02:30:32 UTC (rev 7513)
@@ -1,11 +1,29 @@
-<tool id="swift" name="Swift-tool">
+<tool id="swift" name="Generic-Swift">
   <description>A generic Swift tool to run Swift workflows</description>
   
   <command interpreter="bash">
-  genericswift.sh
-      $site 
-      $script
-      $log_file
+      #if $configuration.mode == "default"
+        genericswift.sh
+            $site 
+            $script
+            $log_file
+    #else
+        genericswift.sh
+            $site 
+            $script
+            $log_file
+            $remoteurl
+            $throttle
+            $project
+            $slots
+            $queue
+            $nodes
+            $nodegranularity
+            $jobspernode
+            $ppn
+            $walltime
+            $maxtime
+    #end if
   </command>
 
   <inputs>
@@ -24,6 +42,7 @@
         <when value="default">
         </when>
         <when value="advanced">
+           <param name="remoteurl" size="50" type="text" value="midway.swift.rcc.uchicago.edu" label="remote url" help="remote resource to run jobs on"></param>
            <param name="throttle" size="5" type="float" value="0.07" label="job throttle" help="number of parallel jobs to run"></param>
            <param name="project" type="text" value="TG-STA110005S" label="Project allocation" help="name/code of project"></param>
            <param name="slots" size="5" type="integer" value="1" label="slots" help="number of scheduler jobs"></param>
@@ -40,4 +59,22 @@
   <outputs>
      <data format="txt" name="log_file" type="data" label="Swift output" />
   </outputs>
+  <help>
+.. class:: warningmark
+
+**TIP**. The data referenced in your Swift script must be absolute path.
+
+-----
+
+**What it does**
+
+This is a generic Swift tool. The tool allows you to select an arbritrary Swift script and run it on the resource of your choice. Currently supported resources are Midway, UC3, Stampede and localhost.
+
+-----
+
+**Example**
+
+Upload a Swift script via get data tools to bring it in history. The tool then will identify Swift scripts and will populate them. Select the resource from the "Execution Location" dropdown.
+
+</help>
 </tool>