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:
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.
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 126.96.36.199. See:
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.
- Initial version (working prototype, using MIRA 3.2.1)
- Improve capture of stdout/stderr (should see it as it runs)
- 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)
- Fix problem with backbone arguments inroduced in v0.0.3
- 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)
- Tell MIRA to use /tmp for temporary files
- Tell MIRA to ignore long read names (otherwise it aborts)
- Automated installation of the 64 bit Linux MIRA binary.
- 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
- Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
- Correct path issue in automated dependency installation
This script and related tools were initially developed on the following hg branch:
Development has now moved to a dedicated GitHub repository:
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
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
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