diff README.rst @ 21:dfaea053e32f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c

--- a/README.rst	Sun May 31 09:05:57 2015 -0400
+++ b/README.rst	Tue Jun 16 23:43:39 2015 -0400
@@ -14,8 +14,8 @@
 Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these.  It creates a large zip archive with all search results, the original database and spectra.  This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
 
 
-Configuration
--------------
+General Requirements
+--------------------
 
 This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
 
@@ -27,7 +27,20 @@
 
 It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.
 
-Note:
+MSAmanda on linux
+-----------------
+
+Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required.  If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually.
+  
+On ubuntu Mono can be installed as follows
+
+	sudo apt-get install mono-runtime
+	sudo apt-get install libmono-system-core4.0-cil
+
+For more help on installing Mono please see http://www.mono-project.com/download. 
+
+Note
+----
 
 - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.
 
@@ -75,4 +88,6 @@
 * Cody Wang
 * Fred Sadler
 * John Chilton <[e-mail]>
+* Gerben Menschaert
+* Elvis Ndah
 * Minnesota Supercomputing Institute, Univeristy of Minnesota