Mercurial > repos > peterjc > mira_assembler
comparison tools/mira_3_4/mira.txt @ 8:4266cccbb45a draft
Uploaded v0.0.7 take 2, fixed path in installation
| author | peterjc |
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| date | Wed, 24 Apr 2013 12:43:17 -0400 |
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| 7:4d3f94dfb857 | 8:4266cccbb45a |
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| 1 Galaxy tool to wrap the MIRA sequence assembly program (v3.4) | |
| 2 ============================================================= | |
| 3 | |
| 4 This tool is copyright 2011-2013 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 separated file for use in Galaxy). | |
| 11 | |
| 12 | |
| 13 Automated Installation | |
| 14 ====================== | |
| 15 | |
| 16 This should be straightforward, Galaxy should automatically download and | |
| 17 install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper, | |
| 18 and run any tests. | |
| 19 | |
| 20 | |
| 21 Manual Installation | |
| 22 =================== | |
| 23 | |
| 24 There are just two Galaxy files to install: | |
| 25 | |
| 26 * mira.py (the Python script) | |
| 27 * mira.xml (the Galaxy tool definition) | |
| 28 | |
| 29 The suggested location is a new tools/mira_3_4 folder. You will also need to | |
| 30 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do | |
| 31 this to tools_conf.xml.sample in order to run any tests: | |
| 32 | |
| 33 <tool file="mira_3_4/mira.xml" /> | |
| 34 | |
| 35 You will also need to install MIRA, we used version 3.4.1.1. See: | |
| 36 | |
| 37 http://chevreux.org/projects_mira.html | |
| 38 http://sourceforge.net/projects/mira-assembler/ | |
| 39 | |
| 40 WARNING: This tool was developed to construct viral genome assembly and | |
| 41 mapping pipelines, for which the run time and memory requirements are | |
| 42 negligible. For larger tasks, be aware that MIRA can require vast amounts | |
| 43 of RAM and run-times of over a week are possible. This tool wrapper makes | |
| 44 no attempt to spot and reject such large jobs. | |
| 45 | |
| 46 | |
| 47 History | |
| 48 ======= | |
| 49 | |
| 50 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) | |
| 51 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) | |
| 52 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later | |
| 53 (some other switches changed, e.g. -OUT rrol to rrot, which | |
| 54 means the wrapper no longer works with MIRA 3.2.x) | |
| 55 - The contig summary file (TCS file) was removed in MIRA 3.4 | |
| 56 - Report all missing output files (not just first missing one) | |
| 57 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3 | |
| 58 v0.0.5 - Implement the <version_command> tag to record the wrapper | |
| 59 version and the MIRA version being used. | |
| 60 - Check using MIRA 3.4 (later versions have a different API) | |
| 61 v0.0.6 - Tell MIRA to use /tmp for temporary files | |
| 62 - Tell MIRA to ignore long read names (otherwise it aborts) | |
| 63 v0.0.7 - Automated installation of the 64 bit Linux MIRA binary. | |
| 64 | |
| 65 | |
| 66 Developers | |
| 67 ========== | |
| 68 | |
| 69 This script and related tools are being developed on the following hg branch: | |
| 70 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 71 | |
| 72 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
| 73 the following command from the Galaxy root folder: | |
| 74 | |
| 75 tar -czf mira_wrapper.tar.gz tools/mira_3_4/mira.* | |
| 76 | |
| 77 Check this worked: | |
| 78 | |
| 79 $ tar -tzf mira_wrapper.tar.gz | |
| 80 tools/mira_3_4/mira.py | |
| 81 tools/mira_3_4/mira.txt | |
| 82 tools/mira_3_4/mira.xml | |
| 83 | |
| 84 | |
| 85 Licence (MIT/BSD style) | |
| 86 ======================= | |
| 87 | |
| 88 Permission to use, copy, modify, and distribute this software and its | |
| 89 documentation with or without modifications and for any purpose and | |
| 90 without fee is hereby granted, provided that any copyright notices | |
| 91 appear in all copies and that both those copyright notices and this | |
| 92 permission notice appear in supporting documentation, and that the | |
| 93 names of the contributors or copyright holders not be used in | |
| 94 advertising or publicity pertaining to distribution of the software | |
| 95 without specific prior permission. | |
| 96 | |
| 97 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 98 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 99 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 100 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 101 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 102 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 103 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 104 OR PERFORMANCE OF THIS SOFTWARE. |