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+Galaxy wrapper for the MIRA assembly program (v4.9) mirabait
+============================================================
+
+This tool is copyright 2011-2015 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 is a Galaxy wrapper for ``mirabait`` from the MIRA 4.9 assembly suite.
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
+
+Development/test previews are available from the Galaxy Test Tool Shed at:
+http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
+
+It is part of a suite for all the MIRA 4.9 tools:
+TODO...
+
+A separate wrapper for MIRA v4.0 is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
+
+
+Automated Installation
+======================
+
+This should be straightforward. Via the Tool Shed, Galaxy should automatically
+install the precompiled binaries for MIRA v4.9.5, and offer to run any tests.
+
+
+Manual Installation
+===================
+
+There are various Python and XML files to install into Galaxy:
+
+* ``mira4_9_mirabait.xml`` (the Galaxy tool definition for mirabait)
+* ``mira_check_version.py`` (Python helper script)
+
+The suggested location is a new ``tools/mira4_9`` folder. You will
+also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
+tool::
+
+  <tool file="mira4_9/mirabait/mira4_9_mirabait.xml" />
+  ...
+
+You will also need to install MIRA 4.9, we used version 4.9.5, and define the
+environment variable ``$MIRA4_9`` pointing at the folder containing the
+binaries. See:
+
+* http://chevreux.org/projects_mira.html
+* http://sourceforge.net/projects/mira-assembler/
+
+You may wish to use different cluster setups for the de novo and mapping
+tools, see above.
+
+You will also need to install samtools (for generating a BAM file from MIRA's
+SAM output).
+
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    $ ./run_tests.sh -id mira4_9_mirabait
+    ...
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version for MIRA 4.9.5, based on wrapper for v4.0.2
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on a dedicated GitHub repository:
+https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9
+
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_update -t testtoolshed --check_diff tools/mira4_9/
+    ...
+
+or::
+
+    $ planemo shed_update -t toolshed --check_diff tools/mira4_9/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only mira4_9/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    ...
+
+
+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.