diff tools/mira4/README.rst @ 5:ffefb87bd414 draft

Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)

--- a/tools/mira4/README.rst	Fri Oct 11 04:28:45 2013 -0400
+++ b/tools/mira4/README.rst	Tue Oct 15 12:07:34 2013 -0400
@@ -1,5 +1,5 @@
-Galaxy tool to wrap the MIRA sequence assembly program (v4.0)
-=============================================================
+Galaxy wrapper for the MIRA assembly program (v4.0)
+===================================================
 
 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
@@ -11,6 +11,11 @@
 It is available from the Galaxy Tool Shed at:
 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler 
 
+It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
+
+A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
 
 Automated Installation
 ======================
@@ -23,9 +28,7 @@
 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
 Consult the Galaxy adminstration documentation for your cluster setup.
 
-WARNING: This tool was developed to construct viral genome assembly and
-mapping pipelines, for which the run time and memory requirements are
-negligible. For larger tasks, be aware that MIRA can require vast amounts
+WARNING: For larger tasks, be aware that MIRA can require vast amounts
 of RAM and run-times of over a week are possible. This tool wrapper makes
 no attempt to spot and reject such large jobs.
 
@@ -50,7 +53,7 @@
   <tool file="mira4/mira4_de_novo.xml" />
   <tool file="mira4/mira4_mapping.xml" />
 
-You will also need to install MIRA, we used version 4.0 RC3. See:
+You will also need to install MIRA, we used version 4.0 RC4. See:
 
 * http://chevreux.org/projects_mira.html
 * http://sourceforge.net/projects/mira-assembler/
@@ -65,7 +68,7 @@
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
-v0.0.1  - Initial version (prototype for MIRA 4.0 RC3, based on wrapper for v3.4)
+v0.0.1  - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
 ======= ======================================================================