Mercurial > repos > pjbriggs > weeder2

comparison README.rst @ 0:fb7e680232af draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v2.0.2
author pjbriggs
date Mon, 05 Mar 2018 06:21:11 -0500
parents
children 79f075dc6cfb
comparison
equal deleted inserted replaced
-1:000000000000 0:fb7e680232af
1 weeder2: motif discovery in sequences from coregulated genes of a single species
2 ================================================================================
3
4 Galaxy tool for the Weeder2 motif discovery package:
5
6 - Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP
7 for the Discovery of Enriched Transcription Factor Binding Site Motifs in
8 Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31.
9 http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full
10
11 See http://159.149.160.51/modtools/
12
13 Automated installation
14 ======================
15
16 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
17 the Weeder2 program and data, and setting the appropriate environment variables.
18
19 Manual Installation
20 ===================
21
22 There are two files to install:
23
24 - ``weeder2_wrapper.xml`` (the Galaxy tool definition)
25 - ``weeder2_wrapper.sh`` (the shell script wrapper)
26
27 The suggested location is in a ``tools/weeder2/`` folder. You will then
28 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
29 by adding the line:
30
31 <tool file="weeder2/weeder2_wrapper.xml" />
32
33 You also need to make a copy of the ``weeder2.loc`` file (a sample version is
34 provided here) which lists the species for which frequency files are available.
35 This file should be placed in the ``tool-data`` directory of your Galaxy
36 installation.
37
38 Additionally you will need to install ``weeder2`` from:
39
40 - http://159.149.160.51/modtools/downloads/weeder2.html
41
42 The tool wrapper uses the following environment variables in order to find the
43 appropriate files:
44
45 - ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory
46
47 Also the directory holding the Weeder2 executables should be on your ``PATH``.
48
49 Functional tests
50 ================
51
52 If you want to run the functional tests, copy the sample test files under
53 sample test files under Galaxy's ``test-data/`` directory. Then:
54
55 ./run_tests.sh -id weeder2
56
57 You will need to have set the environment variables above.
58
59 Reference Data
60 ==============
61
62 Weeder2 requires reference data in the form of frequency files for each
63 species of interest. A set of reference files is provided as part of the
64 Weeder2 installation.
65
66 Additional frequency files can be generated for novel species using the
67 ``w2frequency_maker`` utility available via:
68
69 - http://159.149.160.51/weederaddons/weeder2freq.html
70
71 This page also explains what input data should be used.
72
73 The location of the additional frequency files can then be specified by
74 adding them to the ``weeder2.loc`` file (see above).
75
76 History
77 =======
78
79 ========== ======================================================================
80 Version Changes
81 ---------- ----------------------------------------------------------------------
82 2.0.2 - Drop ``tool_dependencies.xml`` & use conda to resolve dependencies
83 2.0.1 - Explicitly specify frequency files in ``weeder2.loc``.
84 2.0.0 - Initial version
85 ========== ======================================================================
86
87
88 Developers
89 ==========
90
91 This tool is developed on the following GitHub repository:
92 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2
93
94 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
95 the ``package_weeder2.sh`` script.
96
97
98 Licence (MIT)
99 =============
100
101 Permission is hereby granted, free of charge, to any person obtaining a copy
102 of this software and associated documentation files (the "Software"), to deal
103 in the Software without restriction, including without limitation the rights
104 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
105 copies of the Software, and to permit persons to whom the Software is
106 furnished to do so, subject to the following conditions:
107
108 The above copyright notice and this permission notice shall be included in
109 all copies or substantial portions of the Software.
110
111 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
112 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
113 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
114 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
115 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
116 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
117 THE SOFTWARE.