Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/README.rst @ 4:df86ed992a1b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded preview 4, lots of work on mapping
author peterjc
date Fri, 11 Oct 2013 04:28:45 -0400
parents c7538ae82a24
children ffefb87bd414
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
c7538ae82a24 Uploaded v0.0.1 preview 3, fixed version numbers
peterjc
parents: 0
diff changeset
1 Galaxy tool to wrap the MIRA sequence assembly program (v4.0)
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
2 =============================================================
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
3
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
6 See the licence text below (MIT licence).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
7
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
8 This tool is a short Python script (to collect the MIRA output and move it
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
9 to where Galaxy expects the files) and associated Galaxy wrapper XML file.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
10
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
11 It is available from the Galaxy Tool Shed at:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
13
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
14
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
15 Automated Installation
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
16 ======================
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
17
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
18 This should be straightforward. Via the Tool Shed, Galaxy should automatically
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
19 install the 'mira' datatype, download and install the precompiled binary for
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
20 MIRA v4.0 for the Galaxy wrapper, and run any tests.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
21
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
22 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
23 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
24 Consult the Galaxy adminstration documentation for your cluster setup.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
25
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
26 WARNING: This tool was developed to construct viral genome assembly and
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
27 mapping pipelines, for which the run time and memory requirements are
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
28 negligible. For larger tasks, be aware that MIRA can require vast amounts
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
29 of RAM and run-times of over a week are possible. This tool wrapper makes
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
30 no attempt to spot and reject such large jobs.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
31
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
32
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
33 Manual Installation
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
34 ===================
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
35
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
36 First install the 'mira' datatype for Galaxy, available here:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
37
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
38 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
39
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
40 There are just three Galaxy files to install:
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
41
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
42 * mira4.py (the Python script)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
43 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
44 * mira4_mapping.xml (the Galaxy tool definition for mapping usage)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
45
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
46 The suggested location is a new tools/mira4 folder. You will also need to
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
47 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
48 this to tools_conf.xml.sample in order to run any tests::
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
49
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
50 <tool file="mira4/mira4_de_novo.xml" />
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
51 <tool file="mira4/mira4_mapping.xml" />
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
52
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
53 You will also need to install MIRA, we used version 4.0 RC3. See:
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
54
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
55 * http://chevreux.org/projects_mira.html
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
56 * http://sourceforge.net/projects/mira-assembler/
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
57
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
58 You may wish to use different cluster setups for the de novo and mapping
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
59 tools, see above.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
60
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
61
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
62 History
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
63 =======
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
64
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
65 ======= ======================================================================
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
66 Version Changes
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
67 ------- ----------------------------------------------------------------------
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
68 v0.0.1 - Initial version (prototype for MIRA 4.0 RC3, based on wrapper for v3.4)
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
69 ======= ======================================================================
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
70
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
71
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
72 Developers
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
73 ==========
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
74
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
75 Development is on a dedicated GitHub repository:
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
76 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
77
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
79 the following command from the Galaxy root folder::
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
80
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
81 $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
82
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
83 Check this worked::
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
84
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
85 $ tar -tzf mira4_wrapper.tar.gz
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
86 tools/mira4/README.rst
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
87 tools/mira4/mira4_de_novo.xml
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
88 tools/mira4/mira4_mapping.xml
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
89 tools/mira4/mira4.py
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
90 tools/mira4/tool_dependencies.xml
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
91 test-data/tvc_mini.fastq
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
92 test-data/tvc_contigs.fasta
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
93 test-data/tvc_map_ref_strain.fasta
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 3
diff changeset
94 test-data/tvc_map_same_strain.fasta
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
95
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
96
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
97 Licence (MIT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
98 =============
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
99
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
100 Permission is hereby granted, free of charge, to any person obtaining a copy
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
101 of this software and associated documentation files (the "Software"), to deal
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
102 in the Software without restriction, including without limitation the rights
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
103 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
104 copies of the Software, and to permit persons to whom the Software is
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
105 furnished to do so, subject to the following conditions:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
106
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
107 The above copyright notice and this permission notice shall be included in
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
108 all copies or substantial portions of the Software.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
109
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
110 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
111 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
112 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
113 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
114 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
115 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
116 THE SOFTWARE.