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1 RnaChipIntegrator: integrated analysis of gene expression and ChIP data
2 =======================================================================
3
4 Galaxy tool wrappers for running the RnaChipIntegrator program
5 (http://fls-bioinformatics-core.github.com/RnaChipIntegrator/) for integrated
6 analyses of gene expression and ChIP data.
7
8 There are two tools available that are built around RnaChipIntegrator:
9
10 - General RnaChipIntegrator tool that allows any peaks to be analysed against
11 any gene list
12 - A "cannonical gene" variant which allows ChIP peaks to be analysed against a
13 list of cannonical genes for different genomes
14
15 Automated installation
16 ======================
17
18 Installation via the Galaxy Tool Shed will take of installing the tool wrapper
19 and the RnaChipIntegrator programs, installing the .loc files, and setting the
20 appropriate environment variables.
21
22 Manual Installation
23 ===================
24
25 There are three files to install:
26
27 - ``rnachipintegrator_wrapper.xml`` (the Galaxy tool definition for general usage)
28 - ``rnachipintegrator_canonical_genes.xml`` (tool definition for the "canonical
29 gene" variant)
30 - ``rnachipintegrator_wrapper.sh`` (the shell script wrapper)
31
32 The suggested location is in a ``tools/rnachipintegrator/`` folder. You will then
33 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
34 by adding the lines:
35
36 <tool file="rnachipintegrator/rnachipintegrator_wrapper.xml" />
37 <tool file="rnachipintegrator/rnachipintegrator_canonical_genes.xml" />
38
39 You will also need to install the RnaChipIntegrator program:
40
41 - http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
42
43 In addition for the cannonical gene and histone modification variants, it's
44 necessary to copy the .loc.sample files to .loc Galaxy's ``tool-data`` folder:
45
46 - **Cannonical genes**: its necessary to manually acquire cannonical gene
47 list files from UCSC and then add appropriate references in the
48 ``rnachipintegrator_canonical_genes.loc`` file.
49
50 If you want to run the functional tests, copy the sample test files under
51 ``test-data`` to Galaxy's ``test-data/`` directory. Then:
52
53 ./run_tests.sh -id fls_rnachipintegrator_wrapper
54
55
56 How to get canonical gene data
57 ==============================
58
59 Getting canonical gene info from UCSC is covered in the screencast at
60 http://blog.openhelix.eu/?p=6097
61
62 In summary:
63
64 - **UCSC genome browser:** if multiple versions of each gene are visible (e.g.
65 if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000)
66 then:
67
68 - Scroll down to the Gene & Gene Prediction section
69 - Click on the UCSC genes link
70 - Uncheck the tickbox next to splice variants and resubmit to view without
71 duplicates.
72
73 - **UCSC table browser:** to obtain the canonical set of genes from the table
74 browser:
75
76 - Select knownCanonical from the table menu
77 - Select selected fields from primary & related tables from the output format menu
78 - Click on Get output
79 - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the
80 'knownCanonical' table plus 'geneSymbol' from the kgXref table.)
81 - Click on Get output to get the data for download
82
83 (Hint: to also get strand direction information i.e. +/-, also allow selection
84 from the refGene table, and select the strand field.)
85
86
87 Note on Excel output files and Galaxy
88 =====================================
89
90 RnaChipIntegrator produces an Excel spreadsheet as one of its outputs,
91 however Galaxy is not currently set up by default to handle these.
92
93 To enable Excel (XLS) output file handling in Galaxy, edit the
94 ``datatypes_conf.xml`` file and add:
95
96 <datatype extension="xlsx" type="galaxy.datatypes.binary:Binary" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
97
98 Restarting Galaxy should mean that the browser correctly handles Excel outputs
99 from RnaChipIntegrator.
100
101 History
102 =======
103
104 ========== ======================================================================
105 Version Changes
106 ---------- ----------------------------------------------------------------------
107 1.0.0.0 - Update to use latest ``RnaChipIntegrator`` version 1.0.0.
108 0.5.0-0 - Significant update to bring tools in line with
109 ``RnaChipIntegrator`` version 0.5.0, including removing the
110 distinction between 'regions' and 'summits' for input peaks,
111 and otherwise attempting to simplify the tools for users.
112 0.4.4-0 - Initial version pushed to toolshed
113 ========== ======================================================================
114
115
116 Developers
117 ==========
118
119 This tool is developed on the following GitHub repository:
120 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator
121
122 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
123 the ``package_rnachipintegrator_wrapper.sh`` script.
124
125
126 Licence (MIT)
127 =============
128
129 Permission is hereby granted, free of charge, to any person obtaining a copy
130 of this software and associated documentation files (the "Software"), to deal
131 in the Software without restriction, including without limitation the rights
132 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
133 copies of the Software, and to permit persons to whom the Software is
134 furnished to do so, subject to the following conditions:
135
136 The above copyright notice and this permission notice shall be included in
137 all copies or substantial portions of the Software.
138
139 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
140 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
141 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
142 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
143 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
144 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
145 THE SOFTWARE.