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comparison tools/venn_list/README.rst @ 20:016303c30d73 draft

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Fix .shed.yml error leading to wrong upload
author peterjc
date Wed, 13 May 2015 05:05:21 -0400
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children 29d647a7dc39
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19:20eb53c8a79d 20:016303c30d73
1 Galaxy tool to draw a Venn Diagram with up to 3 sets
2 ====================================================
3
4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below.
7
8 This tool is a short Python script (using both the Galaxy and Biopython library
9 functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
10 sets, which are then drawn using the R limma package function vennDiagram
11 (called from Python using rpy).
12
13 This tool is available from the Galaxy Tool Shed at:
14 http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
15
16
17 Automated Installation
18 ======================
19
20 This should be straightforward, Galaxy should automatically download the tool
21 and the Biopython dependency.
22
23 You will still need to install the R/Bioconductor package limma.
24
25
26 Manual Installation
27 ===================
28
29 There are just two files to install:
30
31 * ``venn_list.py`` (the Python script)
32 * ``venn_list.xml`` (the Galaxy tool definition)
33
34 The suggested location is in the Galaxy folder ``tools/plotting`` next to other
35 graph drawing tools, or a dedicated ``tools/venn_list`` directory.
36
37 You will also need to install Biopython 1.54 or later, and the R/Bioconductor
38 package limma. You should already have rpy installed for other Galaxy tools.
39
40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
41 tool. The suggested location is in the "Graph/Display Data" section. Simply add
42 the line::
43
44 <tool file="venn_list/venn_list.xml" />
45
46 If you wish to run the unit tests, also move/copy the ``test-data/`` files
47 under Galaxy's ``test-data/`` folder. Then::
48
49 ./run_tests.sh -id venn_list
50
51
52 History
53 =======
54
55 ======= ======================================================================
56 Version Changes
57 ------- ----------------------------------------------------------------------
58 v0.0.3 - Initial public release.
59 v0.0.4 - Ignore blank lines when loading IDs from tabular files
60 v0.0.5 - Explicit Galaxy error handling of return codes
61 v0.0.6 - Added unit tests.
62 - Use reStructuredText for this README file.
63 - Adopt standard MIT licence.
64 - Updated citation information (Cock et al. 2013).
65 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
66 v0.0.7 - Renamed folder and README file.
67 - Tool definition now embeds citation information.
68 v0.0.8 - Reorder XML elements (internal change only).
69 - Fixed and improved error handling when rpy is not available.
70 - Test output relaxed to cope with more variation in PDF output.
71 - Declare Biopython dependency via the Tool Shed.
72 v0.0.9 - Test with three-way Venn diagram.
73 - Includes testing of failure mode.
74 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
75 ======= ======================================================================
76
77
78 Developers
79 ==========
80
81 This script and related tools were initially developed on the following hg branch:
82 http://bitbucket.org/peterjc/galaxy-central/src/tools
83
84 Development has now moved to a dedicated GitHub repository:
85 https://github.com/peterjc/pico_galaxy
86
87 For pushing a release to the test or main "Galaxy Tool Shed", use the following
88 Planemo commands (which requires you have set your Tool Shed access details in
89 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
90
91 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
92 ...
93
94 or::
95
96 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
97 ...
98
99 To just build and check the tar ball, use::
100
101 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/
102 ...
103 $ tar -tzf shed_upload.tar.gz
104 tools/venn_list/README.rst
105 tools/venn_list/tool_dependencies.xml
106 tools/venn_list/venn_list.py
107 tools/venn_list/venn_list.xml
108 test-data/magic.pdf
109 test-data/rhodopsin_proteins.fasta
110 test-data/venn_list.tabular
111
112
113 Licence (MIT)
114 =============
115
116 Permission is hereby granted, free of charge, to any person obtaining a copy
117 of this software and associated documentation files (the "Software"), to deal
118 in the Software without restriction, including without limitation the rights
119 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
120 copies of the Software, and to permit persons to whom the Software is
121 furnished to do so, subject to the following conditions:
122
123 The above copyright notice and this permission notice shall be included in
124 all copies or substantial portions of the Software.
125
126 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
127 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
128 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
129 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
130 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
131 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
132 THE SOFTWARE.