Galaxy wrapper for the MIRA assembly program (v4.0)
===================================================

This tool is copyright 2011-2014 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 associated Galaxy wrapper XML file.

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
======================

This should be straightforward. Via the Tool Shed, Galaxy should automatically
install the 'mira' datatype, samtools, and download and install the precompiled
binary for MIRA v4.0.2 for the Galaxy wrapper, and run any tests.

For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
cluster settings for de novo usage (high RAM) and mapping (lower RAM).
Consult the Galaxy adminstration documentation for your cluster setup.

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.


Manual Installation
===================

First install the 'mira' datatype for Galaxy, available here:

* http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes 

There are four Galaxy files to install:

* ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage)
* ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
* ``mira4_convert.xml`` (the Galaxy tool definition for converting MIRA files)
* ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
* ``mira4.py`` (the Python wrapper script)
* ``mira4_convert.py`` (the Python wrapper script for miraconvert)
* ``mira4_bait.py`` (the Python wrapper script for mirabait)
* ``mira4_validator.py`` (the XML parameter validation script)

The suggested location is a new ``tools/mira4`` 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 the tests::

  <tool file="mira4/mira4_de_novo.xml" />
  <tool file="mira4/mira4_mapping.xml" />

You will also need to install MIRA, we used version 4.0.2, and define the
environment variable ``$MIRA4`` 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).

After copying (or symlinking) the ``test-data`` files under Galaxy's ``test-data``
folder, you can run the tests with::

    $ ./run_functional_tests.sh -id mira_4_0_bait
    $ ./run_functional_tests.sh -id mira_4_0_de_novo
    $ ./run_functional_tests.sh -id mira_4_0_mapping
    $ ./run_functional_tests.sh -id mira_4_0_convert


History
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
v0.0.1  - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
v0.0.2  - Include BAM output (using ``miraconvert`` and ``samtools``).
        - Updated to target MIRA 4.0.1
        - Simplified XML to apply input format to output data.
        - Sets temporary folder at run time to respect environment variables
          (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
          previously hard coded as ``/tmp``.
v0.0.3  - Updated to target MIRA 4.0.2
v0.0.4  - Using optparse for the Python wrapper script API
        - Made MAF and BAM outputs optional
        - Include wrapper for ``miraconvert``
======= ======================================================================


Developers
==========

Development is on a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder::

    $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4_convert.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_convert.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/header.mira test-data/empty_file.dat

Check this worked::

    $ tar -tzf mira4_wrapper.tar.gz
    tools/mira4/README.rst
    tools/mira4/mira4_de_novo.xml
    tools/mira4/mira4_mapping.xml
    tools/mira4/mira4_bait.xml
    tools/mira4/mira4_convert.xml
    tools/mira4/mira4.py
    tools/mira4/mira4_make_bam.py
    tools/mira4/mira4_validator.py
    tools/mira4/mira4_convert.py
    tools/mira4/mira4_bait.py
    tools/mira4/tool_dependencies.xml
    tools/mira4/repository_dependencies.xml
    test-data/U13small_m.fastq
    test-data/U13small_m.mira4_de_novo.fasta
    test-data/tvc_mini.fastq
    test-data/tvc_contigs.fasta
    test-data/tvc_map_ref_strain.fasta
    test-data/tvc_map_same_strain.fasta
    test-data/tvc_bait.fasta
    test-data/tvc_mini_bait_pos.fastq
    test-data/tvc_mini_bait_strict.fastq
    test-data/tvc_mini_bait_neg.fastq
    test-data/ecoli.fastq
    test-data/ecoli.mira4_de_novo.fasta
    test-data/header.mira
    test-data/empty_file.dat



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.