changeset 2:c25df71f7b68 default tip

Update to protk 1.2.2

--- a/README	Mon Mar 04 23:52:21 2013 -0500
+++ b/README	Sun Jun 09 08:13:09 2013 -0500
@@ -5,14 +5,42 @@
 
 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:
 
-- The ability to download files (an internet connection) curl wget
-- 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
+- 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 
+	installed but this will fail if there are unsatified system dependencies.
+	Alternatively you can pre-install rvm by following instructions at https://rvm.io/rvm/install/ 
+	before you proceed. Protk should work with rvm installed as root or as a local user.
+	This option has the advantage of allowing you control over how rvm is installed in your system.
+
+	(For example. Installing rvm as root user)
+
+	curl -L https://get.rvm.io | sudo bash -s stable
+	sudo usermod -a -G rvm yourusername
+
+	(logout and log back in and then execute the following comand to preinstall ruby and its dependencies)
+
+	rvm install --autolibs=3 1.9.3
+
+

--- a/tool_dependencies.xml	Mon Mar 04 23:52:21 2013 -0500
+++ b/tool_dependencies.xml	Sun Jun 09 08:13:09 2013 -0500
@@ -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>
@@ -18,12 +18,7 @@
         <readme>
             This package installs the protk rubygem which provides facilities for running various proteomics tools via galaxy. 
 
-            Installation of this package requires that you have the following packages (or equivalents) installed gcc g++ patch zlib zlib-devel libyaml-devel libffi-devel  openssl-devel  make  bzip2  autoconf  automake  libtool  bison  iconv-devel libxml2 libxml2-devel zlib zlib-devel bzip2 make
-
             For more about protk see https://bitbucket.org/iracooke/protk
-
-            In order to install ruby and the protk rubygem this package will install rvm (http://rvm.io) to the home directory of your galaxy user at ~/.rvm (if rvm is not already installed). 
-            The protk rubygem is installed in its own gemset and will not interfere with other ruby installations or ruby gems
         </readme>
     </package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>