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+Galaxy wrapper for the MIRA 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 (MIT licence).
+
+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).
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+
+
+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/mira3 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="mira3/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 initially 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
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+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.
+v0.0.8  - Basic unit test added (but commented out due to Galaxy issue).
+        - Link to Tool Shed added to help text and this documentation.
+        - Use reStructuredText for this README file.
+        - Adopted standard MIT licence.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.9  - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
+        - Correct path issue in automated dependency installation
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
+
+Check this worked::
+
+    $ tar -tzf mira3_wrapper.tar.gz
+    tools/mira3/README.rst
+    tools/mira3/mira.xml
+    tools/mira3/mira.py
+    tools/mira3/tool_dependencies.xml
+    test-data/tvc_mini.fastq
+    test-data/tvc_contigs.fasta
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.