[Swift-commit] r7808 - SwiftApps/swift-galaxy

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-04-28 15:27:07 -0500 (Mon, 28 Apr 2014)
New Revision: 7808

Modified:
   SwiftApps/swift-galaxy/README
Log:
update galaxy swift tutorial

Modified: SwiftApps/swift-galaxy/README
===================================================================
--- SwiftApps/swift-galaxy/README	2014-04-27 21:22:48 UTC (rev 7807)
+++ SwiftApps/swift-galaxy/README	2014-04-28 20:27:07 UTC (rev 7808)
@@ -39,6 +39,9 @@
 
 Installation
 -------------
+This installation recipe assumes that you have Galaxy preinstalled. If not,
+installation instructions for Galaxy can be found
+https://wiki.galaxyproject.org/Admin/GetGalaxy[here].
 
 Step 0. Checkout the swift-galaxy SVN directory as follows:
 
@@ -46,18 +49,18 @@
 svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/swift-galaxy
 ----
 
-Step 1. Create a symbolic link of 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. Create a symbolic link to the +swift-galaxy/swift+ directory from
+galaxy's +tools+ directory. For example, if Galaxy top level directory is
++galaxy-dist+ and swift directory is $HOME/swift-galaxy/swift:
 
 ----
-cd galaxy-dist
-ln -s /home/ketan/SwiftApps/swift-galaxy/swift swift
+cd galaxy-dist/tools
+ln -s $HOME/swift-galaxy/swift swift
 ----
 
 The advantage of symbolic links is that as users update the tool directory via
-`svn up`, they need not worry about reinstallation. Everything gets propagated
-to Galaxy.
+`svn up`, they need not worry about reinstallation. Updates in installation
+gets automatically propagated to Galaxy.
 
 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
@@ -66,7 +69,7 @@
 
 ----
 <section name="swift" id="swift">
- <tool file="swift/genswift.xml" />
+ <tool file="swift/tryswift.xml" />
  <tool file="swift/genericswift.xml" />
  <tool file="swift/swiftforeach.xml" />
 </section>
@@ -159,7 +162,7 @@
 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:
+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">