diff README @ 8:2d6671b10919 draft

Updated to support cutadapt version 1.1 (also include automatic dependency installation)

--- a/README	Thu Dec 22 11:46:33 2011 -0500
+++ b/README	Mon Nov 26 17:37:26 2012 -0500
@@ -1,7 +1,18 @@
 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
 
-Installation
-------------
+
+Installation  - Tool Shed
+---------------------------
+
+The recommended way to install cutadapt as a tool in Galaxy is to the use the
+Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed).
+
+This will allow cutadapt to be installed automatically and keep track of older
+versions of cutadapt and the tool wrapper.
+
+
+Installation - Manual
+---------------------
 
 1 - Install the cutadapt package and make sure it is in path for Galaxy
 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
@@ -16,9 +27,16 @@
     See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
 
 
+Configuration of Adapters
+-------------------------
+
+A list of predefined adapters may be specified in the fastx_clipper_sequences.txt
+file which resides in the tool-data directory underneath the Galaxy root.  A sample
+file is provided.
+
+
 Limitations
 -----------
 
 Colorspace data support is not implemented
-Prefix and Suffix to read names not implemented
-Length-tag addition to read name not implemented
+Name adapters support is not implemented