Mercurial > repos > peterjc > mira_assembler
view tools/sr_assembly/mira.txt @ 4:117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
The Galaxy wrapper will no longer work with MIRA v3.2.x - if you are still using the old version of MIRA, please continue to use v0.0.2 of the wrapper.
author | peterjc |
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date | Wed, 21 Dec 2011 11:33:19 -0500 |
parents | 298f5c1d9521 |
children | 216bf640baaf |
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Galaxy tool to wrap the MIRA sequence assembly program ====================================================== This tool is copyright 2011 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This tool is a short Python script (to collect the MIRA output and move it to where Galaxy expects the files, and convert MIRA's TCS file into a tab separated file for use in Galaxy). There are just two files to install: * mira.py (the Python script) * mira.xml (the Galaxy tool definition) The suggested location is the tools/sr_assembly folder. You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool and also do this to tools_conf.xml.sample in order to run any tests: <tool file="sr_assembly/mira.xml" /> You will also need to install MIRA, we used version 3.4.0. See: http://chevreux.org/projects_mira.html http://sourceforge.net/projects/mira-assembler/ WARNING: This tool was developed to construct viral genome assembly and mapping pipelines, for which the run time and memory requirements are negligible. For larger tasks, be aware that MIRA can require vast amounts of RAM and run-times of over a week are possible. This tool wrapper makes no attempt to spot and reject such large jobs. History ======= v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later (some other switched changed, e.g. -OUT rrol to rrot, which means the wrapper no longer works with MIRA 3.2.x) - The contig summary file (TCS file) was removed in MIRA 3.4 - Report all missing output files (not just first missing one) Developers ========== This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.* Check this worked: $ tar -tzf mira_wrapper.tar.gz tools/sr_assembly/mira.py tools/sr_assembly/mira.txt tools/sr_assembly/mira.xml Licence (MIT/BSD style) ======================= Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.