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.