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Repository 'mira_assembler'
http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
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Assemble with MIRA. Takes Sanger, Roche, and Illumina data
Wrapper for core functionality of assembly tool MIRA 3.4.

Sanger capillary, Roche 454, Ion Torrent and Solexa/Illumina data, and reference backbone sequences are all accepted as inputs.

The key MIRA output files are captured, but the other files are deleted when the job finishes.

WARNING: This was written to write viral genome assembly and mapping pipelines, and while it should work for larger organisms the computational load would be much higher. Proceed with caution!
10:a2fb1e67bd11
peterjc
True
442

Repository README files - may contain important installation or license information

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:

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.

Dependencies of this repository

Name Version Type
MIRA 3.4.1.1 package

Contents of this repository

Name Description Version
Assemble with MIRA v3.4 Takes Sanger, Roche, Illumina, and Ion Torrent data 0.0.8

Automated tool test results

Time tested: 2014-04-17 15:12:34
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 13085:c05752549163
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: mira_assembler
Tool version: 0.0.8
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.8
Missing components:
Functional test definitions missing for mira_assembler.

Categories
Assembly
Next Gen Mappers