Mercurial > repos > peterjc > mira_assembler

annotate tools/sr_assembly/mira.txt @ 2:8bddbb4b2575 draft

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Uploaded v0.0.6
author peterjc
date Wed, 24 Apr 2013 11:52:10 -0400
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d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 Galaxy tool to wrap the MIRA sequence assembly program
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2 ======================================================
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3
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4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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8 This tool is a short Python script (to collect the MIRA output and move it
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9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab
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10 separated file for use in Galaxy). There are just two files to install:
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12 * mira.py (the Python script)
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13 * mira.xml (the Galaxy tool definition)
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15 The suggested location is the tools/sr_assembly folder. You will also need to
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16 modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
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17 this to tools_conf.xml.sample in order to run any tests:
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19 <tool file="sr_assembly/mira.xml" />
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21 You will also need to install MIRA, we used version 3.4.0. See:
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23 http://chevreux.org/projects_mira.html
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24 http://sourceforge.net/projects/mira-assembler/
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26 WARNING: This tool was developed to construct viral genome assembly and
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27 mapping pipelines, for which the run time and memory requirements are
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28 negligible. For larger tasks, be aware that MIRA can require vast amounts
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29 of RAM and run-times of over a week are possible. This tool wrapper makes
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30 no attempt to spot and reject such large jobs.
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33 History
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34 =======
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35
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36 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
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37 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
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38 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
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39 (some other switches changed, e.g. -OUT rrol to rrot, which
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40 means the wrapper no longer works with MIRA 3.2.x)
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41 - The contig summary file (TCS file) was removed in MIRA 3.4
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42 - Report all missing output files (not just first missing one)
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43 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
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44 v0.0.5 - Implement the <version_command> tag to record the wrapper
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45 version and the MIRA version being used.
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46 - Check using MIRA 3.4 (later versions have a different API)
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47 v0.0.6 - Tell MIRA to use /tmp for temporary files
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48 - Tell MIRA to ignore long read names (otherwise it aborts)
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51 Developers
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52 ==========
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53
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54 This script and related tools are being developed on the following hg branch:
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55 http://bitbucket.org/peterjc/galaxy-central/src/tools
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57 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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58 the following command from the Galaxy root folder:
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60 tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.*
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62 Check this worked:
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63
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64 $ tar -tzf mira_wrapper.tar.gz
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65 tools/sr_assembly/mira.py
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66 tools/sr_assembly/mira.txt
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67 tools/sr_assembly/mira.xml
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70 Licence (MIT/BSD style)
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71 =======================
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72
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73 Permission to use, copy, modify, and distribute this software and its
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74 documentation with or without modifications and for any purpose and
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75 without fee is hereby granted, provided that any copyright notices
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76 appear in all copies and that both those copyright notices and this
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77 permission notice appear in supporting documentation, and that the
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78 names of the contributors or copyright holders not be used in
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79 advertising or publicity pertaining to distribution of the software
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80 without specific prior permission.
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81
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82 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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83 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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84 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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85 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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86 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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87 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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88 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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89 OR PERFORMANCE OF THIS SOFTWARE.