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comparison tools/sr_assembly/mira.txt @ 4:117cce3296af

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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
date Wed, 21 Dec 2011 11:33:19 -0500
parents 298f5c1d9521
children 216bf640baaf
comparison
equal deleted inserted replaced
3:298f5c1d9521 4:117cce3296af
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 This tool is a short Python script (to collect the MIRA output and move it 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 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: 10 separated file for use in Galaxy). There are just two files to install:
11 11
12 * mira.py (the Python script) 12 * mira.py (the Python script)
13 * mira.xml (the Galaxy tool definition) 13 * mira.xml (the Galaxy tool definition)
14 14
15 The suggested location is the tools/sr_assembly folder. You will also need to 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 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: 17 this to tools_conf.xml.sample in order to run any tests:
18 18
19 <tool file="sr_assembly/seq_primer_clip.xml" /> 19 <tool file="sr_assembly/mira.xml" />
20 20
21 You will also need to install MIRA, we used version 3.2.1. See: 21 You will also need to install MIRA, we used version 3.4.0. See:
22 22
23 http://chevreux.org/projects_mira.html 23 http://chevreux.org/projects_mira.html
24 http://sourceforge.net/projects/mira-assembler/ 24 http://sourceforge.net/projects/mira-assembler/
25 25
26 WARNING: This tool was developed to construct viral genome assembly and 26 WARNING: This tool was developed to construct viral genome assembly and
31 31
32 32
33 History 33 History
34 ======= 34 =======
35 35
36 v0.0.1 - Initial version (working prototype) 36 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
37 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) 37 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
38 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
39 (some other switched changed, e.g. -OUT rrol to rrot, which
40 means the wrapper no longer works with MIRA 3.2.x)
41 - The contig summary file (TCS file) was removed in MIRA 3.4
42 - Report all missing output files (not just first missing one)
38 43
39 44
40 Developers 45 Developers
41 ========== 46 ==========
42 47