changeset 1:32c643142290 default tip

Fix

--- a/README	Wed May 08 03:08:10 2013 -0400
+++ b/README	Thu Jun 06 15:34:30 2013 +1000
@@ -5,14 +5,27 @@
 
 The installer does the following
 1. Downloads an install script from dropbox
-2. Installs ruby version manager (rvm) into the home directory of the galaxy user (ie at ~/.rvm)
+2. Installs ruby version manager (rvm) into the home directory of the galaxy user (ie at $HOME/.rvm)
 3. Uses rvm to download and compile ruby 1.9.3
 4. Creates a gemset to install the protk rubygem
 5. Installs the protk rubygem which involves compiling a libxml extension
 
 System Requirements:
 
-You **MUST** install these packages from the commandline before installing this via galaxy. 
+- General requirements:
+	Many of these requirements are for building rvm and ruby itself. If you have pre-installed 
+	rvm and ruby you should already have most of these installed (See below for pre-installing RVM and Ruby)
+
+	Requires the ability to download files (an internet connection) curl wget
+	Requires basic build tools. 
+	On Ubuntu, package build-essential is usually sufficient
+	On Centos, you should install gcc g++ make autoconf automake libtool pkg-config patch git openssl libreadline6 libreadline6-dev git-core zlib1g zlib1g-dev libssl-dev libc6-dev ncurses-dev bison subversion libxml2 libxml2-dev gawk
+
+- Tested Systems:
+	Ubuntu-12.04-LTS 64 Bit Server With OpenSSH preinstalled:
+
+	Requires
+	build-essential mercurial libreadline6-dev zlib1g-dev libssl-dev libyaml-dev libsqlite3-dev sqlite3 libxml2-dev libxslt1-dev autoconf libgdbm-dev libncurses5-dev automake libtool bison pkg-config libffi-dev
 
 - RVM (Ruby Version Manager)
 	The install script will attempt to install rvm for you if it is not already 
@@ -30,18 +43,4 @@
 
 	rvm install --autolibs=3 1.9.3
 
-- General requirements:
-	Many of these requirements are for building rvm and ruby itself. If you have pre-installed 
-	rvm and ruby you should already have most of these installed 
 
-	Requires the ability to download files (an internet connection) curl wget
-	Requires basic build tools. 
-	On Ubuntu package build-essential is sufficient
-	On Centos you should install gcc g++ make autoconf automake libtool pkg-config patch git openssl libreadline6 libreadline6-dev git-core zlib1g zlib1g-dev libssl-dev libc6-dev ncurses-dev bison subversion libxml2 libxml2-dev gawk
-
-- Tested Systems:
-	Ubuntu-12.04-LTS 64 Bit Server With OpenSSH preinstalled:
-
-	Requires
-	build-essential mercurial libreadline6-dev zlib1g-dev libssl-dev libyaml-dev libsqlite3-dev sqlite3 libxml2-dev libxslt1-dev autoconf libgdbm-dev libncurses5-dev automake libtool bison pkg-config libffi-dev
-

--- a/tool_dependencies.xml	Wed May 08 03:08:10 2013 -0400
+++ b/tool_dependencies.xml	Thu Jun 06 15:34:30 2013 +1000
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="galaxy_protk" version="1.2.0">
+    <package name="galaxy_protk" version="1.2.2">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://dl.dropbox.com/u/226794/galaxy_protk.tar.gz</action>
-                <action type="shell_command">sh install_protk.sh 1.2.0</action>
+                <action type="shell_command">sh install_protk.sh 1.2.2</action>
                 <action type="move_file">
                     <source>install_protk.sh</source>
                     <destination>$INSTALL_DIR</destination>