--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.txt	Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,104 @@
+Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
+=============================================================
+
+This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (to collect the MIRA output and move it
+to where Galaxy expects the files, and convert MIRA's TCS file into a tab
+separated file for use in Galaxy).
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and
+install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
+and run any tests.
+
+
+Manual Installation
+===================
+
+There are just two Galaxy files to install:
+
+* mira.py (the Python script)
+* mira.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/mira_3_4 folder. You will also need to
+modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
+this to tools_conf.xml.sample in order to run any tests:
+
+<tool file="mira_3_4/mira.xml" />
+
+You will also need to install MIRA, we used version 3.4.1.1. See:
+
+http://chevreux.org/projects_mira.html
+http://sourceforge.net/projects/mira-assembler/
+
+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
+of RAM and run-times of over a week are possible. This tool wrapper makes
+no attempt to spot and reject such large jobs.
+
+
+History
+=======
+
+v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
+v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
+v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
+         (some other switches changed, e.g. -OUT rrol to rrot, which
+         means the wrapper no longer works with MIRA 3.2.x)
+       - The contig summary file (TCS file) was removed in MIRA 3.4
+       - Report all missing output files (not just first missing one)
+v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
+v0.0.5 - Implement the <version_command> tag to record the wrapper
+         version and the MIRA version being used.
+       - Check using MIRA 3.4 (later versions have a different API)
+v0.0.6 - Tell MIRA to use /tmp for temporary files
+       - Tell MIRA to ignore long read names (otherwise it aborts)
+v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+tar -czf mira_wrapper.tar.gz tools/mira_3_4/mira.*
+
+Check this worked:
+
+$ tar -tzf mira_wrapper.tar.gz
+tools/mira_3_4/mira.py
+tools/mira_3_4/mira.txt
+tools/mira_3_4/mira.xml
+
+
+Licence (MIT/BSD style)
+=======================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.