Mercurial > repos > peterjc > mira_assembler
annotate tools/sr_assembly/mira.txt @ 5:216bf640baaf draft
Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.
author | peterjc |
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date | Wed, 09 May 2012 12:40:06 -0400 |
parents | 117cce3296af |
children | 3e7eca1f5d04 |
rev | line source |
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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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7 |
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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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117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
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10 separated file for use in Galaxy). There are just two files to install: |
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11 |
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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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14 |
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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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18 |
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117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
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19 <tool file="sr_assembly/mira.xml" /> |
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20 |
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117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
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21 You will also need to install MIRA, we used version 3.4.0. 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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25 |
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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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31 |
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32 |
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33 History |
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34 ======= |
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35 |
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117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
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36 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) |
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298f5c1d9521
Uploaded v0.0.2 of the wrapper, which improves capture of the stdout/stderr log file from MIRA.
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37 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) |
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117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
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38 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later |
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216bf640baaf
Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.
peterjc
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39 (some other switches changed, e.g. -OUT rrol to rrot, which |
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117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
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40 means the wrapper no longer works with MIRA 3.2.x) |
117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
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41 - The contig summary file (TCS file) was removed in MIRA 3.4 |
117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
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42 - Report all missing output files (not just first missing one) |
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216bf640baaf
Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.
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43 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3 |
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44 |
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45 |
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46 Developers |
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47 ========== |
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48 |
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49 This script and related tools are being developed on the following hg branch: |
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50 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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51 |
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52 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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53 the following command from the Galaxy root folder: |
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54 |
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55 tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.* |
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56 |
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57 Check this worked: |
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58 |
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59 $ tar -tzf mira_wrapper.tar.gz |
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60 tools/sr_assembly/mira.py |
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61 tools/sr_assembly/mira.txt |
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62 tools/sr_assembly/mira.xml |
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63 |
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64 |
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65 Licence (MIT/BSD style) |
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66 ======================= |
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67 |
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68 Permission to use, copy, modify, and distribute this software and its |
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69 documentation with or without modifications and for any purpose and |
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70 without fee is hereby granted, provided that any copyright notices |
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71 appear in all copies and that both those copyright notices and this |
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72 permission notice appear in supporting documentation, and that the |
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73 names of the contributors or copyright holders not be used in |
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74 advertising or publicity pertaining to distribution of the software |
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75 without specific prior permission. |
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76 |
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77 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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78 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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79 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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80 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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81 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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82 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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83 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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84 OR PERFORMANCE OF THIS SOFTWARE. |