Mercurial > repos > peterjc > mira_assembler
comparison 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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3:298f5c1d9521 | 4:117cce3296af |
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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 |