Mercurial > repos > pjbriggs > motif_tools
comparison README.rst @ 0:b67ea47730d3 draft
Version 1.0.1.
author | pjbriggs |
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date | Wed, 21 Mar 2018 06:39:41 -0400 |
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children | 764d562755bd |
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1 motif_tools | |
2 =========== | |
3 | |
4 Galaxy tools for various motif-finding utilities developed by Ian Donaldson. | |
5 | |
6 There are five tools available: | |
7 | |
8 * **IUPAC scan and output each match** Returns all matches to a given IUPAC in | |
9 GFF format | |
10 | |
11 * **IUPAC scan and output matches per seq** Counts the matches to a given IUPAC | |
12 | |
13 * **Count unique seq in GFF** Gives the non-redundant count of sequences | |
14 | |
15 * **TFBScluster two TFBS** Identifies clusters of two TFBS | |
16 | |
17 * **TFBScluster three TFBS** Identifies clusters of three TFBS | |
18 | |
19 Automated installation | |
20 ====================== | |
21 | |
22 Installation via the Galaxy Tool Shed will take of installing the tools | |
23 and the underlying dependencies. | |
24 | |
25 Manual Installation | |
26 =================== | |
27 | |
28 To add these to Galaxy put the following lines in tool_conf.xml for each: | |
29 tool that you want:: | |
30 | |
31 <tool file="motif_tools/Scan_IUPAC_output_each_match.xml" /> | |
32 <tool file="motif_tools/Scan_IUPAC_output_matches_per_seq.xml" /> | |
33 <tool file="motif_tools/CountUniqueIDs.xml" /> | |
34 <tool file="motif_tools/TFBScluster_candidates_2TFBS.xml" /> | |
35 <tool file="motif_tools/TFBScluster_candidates_3TFBS.xml" /> | |
36 | |
37 The tools also require Perl and ``Bioperl`` to be installed. | |
38 | |
39 History | |
40 ======= | |
41 | |
42 ========== ===================================================================== | |
43 = | |
44 Version Changes | |
45 ---------- ---------------------------------------------------------------------- | |
46 - 1.0.1 Updates to use conda dependency resolution and tidy up XML | |
47 - 1.0.0 Initial version | |
48 ========== ===================================================================== | |
49 = | |
50 | |
51 Developers | |
52 ========== | |
53 | |
54 This tool is developed on the following GitHub repository: | |
55 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/tools/macs21 | |
56 | |
57 | |
58 Licence (MIT) | |
59 ============= | |
60 | |
61 Permission is hereby granted, free of charge, to any person obtaining a copy | |
62 of this software and associated documentation files (the "Software"), to deal | |
63 in the Software without restriction, including without limitation the rights | |
64 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
65 copies of the Software, and to permit persons to whom the Software is | |
66 furnished to do so, subject to the following conditions: | |
67 | |
68 The above copyright notice and this permission notice shall be included in | |
69 all copies or substantial portions of the Software. | |
70 | |
71 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
72 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
73 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
74 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
75 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
76 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
77 THE SOFTWARE. |