Mercurial > repos > peterjc > mira_assembler
comparison tools/sr_assembly/mira.txt @ 0:03b240624b5a
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 16:23:51 -0400 |
| parents | |
| children | 298f5c1d9521 |
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| -1:000000000000 | 0:03b240624b5a |
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| 1 Galaxy tool to wrap the MIRA sequence assembly program | |
| 2 ====================================================== | |
| 3 | |
| 4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute | |
| 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
| 6 See the licence text below. | |
| 7 | |
| 8 This tool is a short Python script (to collect the MIRA output and move it | |
| 9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab | |
| 10 separate file for use in Galaxy). There are just two files to install: | |
| 11 | |
| 12 * mira.py (the Python script) | |
| 13 * mira.xml (the Galaxy tool definition) | |
| 14 | |
| 15 The suggested location is the tools/sr_assembly folder. You will also need to | |
| 16 modify the tools_conf.xml file to tell Galaxy to offer the tool and also do | |
| 17 this to tools_conf.xml.sample in order to run any tests: | |
| 18 | |
| 19 <tool file="sr_assembly/seq_primer_clip.xml" /> | |
| 20 | |
| 21 You will also need to install MIRA, we used version 3.2.1. See: | |
| 22 | |
| 23 http://chevreux.org/projects_mira.html | |
| 24 http://sourceforge.net/projects/mira-assembler/ | |
| 25 | |
| 26 WARNING: This tool was developed to construct viral genome assembly and | |
| 27 mapping pipelines, for which the run time and memory requirements are | |
| 28 negligible. For larger tasks, be aware that MIRA can require vast amounts | |
| 29 of RAM and run-times of over a week are possible. This tool wrapper makes | |
| 30 no attempt to spot and reject such large jobs. | |
| 31 | |
| 32 | |
| 33 History | |
| 34 ======= | |
| 35 | |
| 36 v0.0.1 - Initial version (working prototype) | |
| 37 | |
| 38 | |
| 39 Developers | |
| 40 ========== | |
| 41 | |
| 42 This script and related tools are being developed on the following hg branch: | |
| 43 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 44 | |
| 45 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
| 46 the following command from the Galaxy root folder: | |
| 47 | |
| 48 tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.* | |
| 49 | |
| 50 Check this worked: | |
| 51 | |
| 52 $ tar -tzf mira_wrapper.tar.gz | |
| 53 tools/sr_assembly/mira.py | |
| 54 tools/sr_assembly/mira.txt | |
| 55 tools/sr_assembly/mira.xml | |
| 56 | |
| 57 | |
| 58 Licence (MIT/BSD style) | |
| 59 ======================= | |
| 60 | |
| 61 Permission to use, copy, modify, and distribute this software and its | |
| 62 documentation with or without modifications and for any purpose and | |
| 63 without fee is hereby granted, provided that any copyright notices | |
| 64 appear in all copies and that both those copyright notices and this | |
| 65 permission notice appear in supporting documentation, and that the | |
| 66 names of the contributors or copyright holders not be used in | |
| 67 advertising or publicity pertaining to distribution of the software | |
| 68 without specific prior permission. | |
| 69 | |
| 70 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 71 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 72 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 73 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 74 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 75 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 76 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 77 OR PERFORMANCE OF THIS SOFTWARE. |