Mercurial > repos > peterjc > mira_assembler

annotate tools/sr_assembly/mira.txt @ 2:73263d5c2c9f

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Remove botched upload (see Galaxy issue 586)
author g2cmnty@test-web1.g2.bx.psu.edu
date Tue, 21 Jun 2011 09:48:11 -0400
parents 03b240624b5a
children 298f5c1d9521
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
1 Galaxy tool to wrap the MIRA sequence assembly program
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 ======================================================
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 See the licence text below.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 This tool is a short Python script (to collect the MIRA output and move it
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 separate file for use in Galaxy). There are just two files to install:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 * mira.py (the Python script)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 * mira.xml (the Galaxy tool definition)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15 The suggested location is the tools/sr_assembly folder. You will also need to
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 this to tools_conf.xml.sample in order to run any tests:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 <tool file="sr_assembly/seq_primer_clip.xml" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 You will also need to install MIRA, we used version 3.2.1. See:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 http://chevreux.org/projects_mira.html
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 http://sourceforge.net/projects/mira-assembler/
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 WARNING: This tool was developed to construct viral genome assembly and
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 mapping pipelines, for which the run time and memory requirements are
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 negligible. For larger tasks, be aware that MIRA can require vast amounts
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 of RAM and run-times of over a week are possible. This tool wrapper makes
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 no attempt to spot and reject such large jobs.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 History
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34 =======
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36 v0.0.1 - Initial version (working prototype)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
38
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
39 Developers
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 ==========
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
41
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
42 This script and related tools are being developed on the following hg branch:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
43 http://bitbucket.org/peterjc/galaxy-central/src/tools
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
44
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
46 the following command from the Galaxy root folder:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
47
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48 tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.*
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50 Check this worked:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 $ tar -tzf mira_wrapper.tar.gz
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53 tools/sr_assembly/mira.py
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 tools/sr_assembly/mira.txt
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 tools/sr_assembly/mira.xml
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58 Licence (MIT/BSD style)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 =======================
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61 Permission to use, copy, modify, and distribute this software and its
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 documentation with or without modifications and for any purpose and
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63 without fee is hereby granted, provided that any copyright notices
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 appear in all copies and that both those copyright notices and this
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65 permission notice appear in supporting documentation, and that the
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 names of the contributors or copyright holders not be used in
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67 advertising or publicity pertaining to distribution of the software
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 without specific prior permission.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 OR PERFORMANCE OF THIS SOFTWARE.