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Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
author peterjc
date Tue, 15 Oct 2013 12:07:34 -0400
parents df86ed992a1b
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4:df86ed992a1b 5:ffefb87bd414
1 Galaxy tool to wrap the MIRA sequence assembly program (v4.0) 1 Galaxy wrapper for the MIRA assembly program (v4.0)
2 ============================================================= 2 ===================================================
3 3
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute 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. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence). 6 See the licence text below (MIT licence).
7 7
9 to where Galaxy expects the files) and associated Galaxy wrapper XML file. 9 to where Galaxy expects the files) and associated Galaxy wrapper XML file.
10 10
11 It is available from the Galaxy Tool Shed at: 11 It is available from the Galaxy Tool Shed at:
12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler 12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
13 13
14 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
15 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
16
17 A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at:
18 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
14 19
15 Automated Installation 20 Automated Installation
16 ====================== 21 ======================
17 22
18 This should be straightforward. Via the Tool Shed, Galaxy should automatically 23 This should be straightforward. Via the Tool Shed, Galaxy should automatically
21 26
22 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate 27 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
23 cluster settings for de novo usage (high RAM) and mapping (lower RAM). 28 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
24 Consult the Galaxy adminstration documentation for your cluster setup. 29 Consult the Galaxy adminstration documentation for your cluster setup.
25 30
26 WARNING: This tool was developed to construct viral genome assembly and 31 WARNING: For larger tasks, be aware that MIRA can require vast amounts
27 mapping pipelines, for which the run time and memory requirements are
28 negligible. For larger tasks, be aware that MIRA can require vast amounts
29 of RAM and run-times of over a week are possible. This tool wrapper makes 32 of RAM and run-times of over a week are possible. This tool wrapper makes
30 no attempt to spot and reject such large jobs. 33 no attempt to spot and reject such large jobs.
31 34
32 35
33 Manual Installation 36 Manual Installation
48 this to tools_conf.xml.sample in order to run any tests:: 51 this to tools_conf.xml.sample in order to run any tests::
49 52
50 <tool file="mira4/mira4_de_novo.xml" /> 53 <tool file="mira4/mira4_de_novo.xml" />
51 <tool file="mira4/mira4_mapping.xml" /> 54 <tool file="mira4/mira4_mapping.xml" />
52 55
53 You will also need to install MIRA, we used version 4.0 RC3. See: 56 You will also need to install MIRA, we used version 4.0 RC4. See:
54 57
55 * http://chevreux.org/projects_mira.html 58 * http://chevreux.org/projects_mira.html
56 * http://sourceforge.net/projects/mira-assembler/ 59 * http://sourceforge.net/projects/mira-assembler/
57 60
58 You may wish to use different cluster setups for the de novo and mapping 61 You may wish to use different cluster setups for the de novo and mapping
63 ======= 66 =======
64 67
65 ======= ====================================================================== 68 ======= ======================================================================
66 Version Changes 69 Version Changes
67 ------- ---------------------------------------------------------------------- 70 ------- ----------------------------------------------------------------------
68 v0.0.1 - Initial version (prototype for MIRA 4.0 RC3, based on wrapper for v3.4) 71 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
69 ======= ====================================================================== 72 ======= ======================================================================
70 73
71 74
72 Developers 75 Developers
73 ========== 76 ==========