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annotate tools/sr_assembly/mira.txt @ 0:d0a5acdf1638

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Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 15:47:17 -0400
parents
children c947750f82fb
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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 separate file for use in Galaxy). There are just two files to install:
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11
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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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/seq_primer_clip.xml" />
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21 You will also need to install MIRA, we used version 3.2.1. See:
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22
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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
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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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
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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36 v0.0.1 - Initial version (working prototype)
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38
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39 Developers
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40 ==========
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41
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42 This script and related tools are being developed on the following hg branch:
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43 http://bitbucket.org/peterjc/galaxy-central/src/tools
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44
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45 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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46 the following command from the Galaxy root folder:
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48 tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.*
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50 Check this worked:
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51
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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52 $ tar -tzf mira_wrapper.tar.gz
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53 tools/sr_assembly/mira.py
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54 tools/sr_assembly/mira.txt
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55 tools/sr_assembly/mira.xml
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57
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58 Licence (MIT/BSD style)
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59 =======================
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60
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61 Permission to use, copy, modify, and distribute this software and its
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62 documentation with or without modifications and for any purpose and
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63 without fee is hereby granted, provided that any copyright notices
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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64 appear in all copies and that both those copyright notices and this
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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65 permission notice appear in supporting documentation, and that the
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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66 names of the contributors or copyright holders not be used in
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67 advertising or publicity pertaining to distribution of the software
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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68 without specific prior permission.
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69
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70 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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71 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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72 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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73 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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74 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
d0a5acdf1638 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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75 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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76 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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77 OR PERFORMANCE OF THIS SOFTWARE.