source: plugins/base1/se.lu.onk.ReplicateError/trunk/README @ 766

Last change on this file since 766 was 766, checked in by Jari Häkkinen, 14 years ago

Addresses #129. Updated configuration files, reworked html result table generation, first version of README.

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1$Id: README 766 2008-09-16 09:22:37Z jari $
2
3= About `se.lu.onk.ReplicateError` =
4
5The `se.lu.onk.ReplicateError` plug-in for BASE is
6
7`se.lu.onk.ReplicateError` is free software. See the file license.txt for
8copying conditions.
9
10The package was created by Johan Enell and is currently maintained by
11Jari Häkkinen.
12
13
14== Downloading ==
15
16`se.lu.onk.ReplicateError` can be obtained from
17
18  http://baseplugins.thep.lu.se/wiki/PluginDownload
19
20
21== Installation ==
22
23''This plug-in is only tested in BASE 2.8 through the
24Base1PluginExecuter but is expected to work also in BASE
251.2.17. Please report failure or success in BASE 1.2 through
26http://baseplugins.thep.lu.se. These installation instructions only
27describe how to get the plug-in to work with the Base1PluginExecuter
28in the latest BASE version 2. BASE 1.2 installers should enable one
29line in files AAtabs.html and WAtabs.html, read the information in
30these short files.''
31
32If you downloaded a binary package you only need to follow these
33instructions. If you prefer to compile the package yourself, read the
34instructions about compiling and creating a distribution before doing
35the installation steps described here.
36
37You need to understand how to install plug-ins in BASE, please refer
38to BASE documentation at http://base.thep.lu.se for general
39instructions on plug-in installation. The BASE documentation contains
40a chapter on plug-ins. If you have read the instructions you should be
41able to follow this path
42{{{
43  # cd /path/to/base/plugins
44  # download ReplicateError-version.tgz
45  # untar ReplicateError-version.tgz
46  # ln -s ReplicateError-version ReplicateError
47}}}
48The symbolical link in the last line above allows for easier change to
49future version of the plug-in.
50{{{
51  # Log in to your BASE as admin
52  # Create one configuration each for across and within assays mode of
53    the ReplciateError plug-in where you select the plug-in defintion
54    files pluginConfigurationAA.base and pluginConfigurationWA.base,
55    respectively. BASE will respond that plug-ins where configured
56    but...
57  # Re-configure the plug-ins without selecting a file, set the
58    `Plugin executables path` and proceed to next window by clicking
59    `Next`. This is explained in the BASE documentation.
60  # In this parameter window set the `Name of executable`. The value
61    of this parameter and `Plugin executables path` should add up to
62    the absolute path to the binaries `runAA` and `runWA`, i.e.,
63    /path/to/base/plugins/ReplicateError/runAA. How this string looks
64    like depends on your plug-in directory structure.
65  # Test the plug-ins and when you are satisfied, share it to your
66    users.
67}}}
68
69
70== Compiling ==
71
72You must checkout the `se.lu.onk.ReplicateError` from the repository,
73follow the instructions below. Then download and untar the
74`se.lu.onk.BaseFile` package available from
75http://baseplugins.thep.lu.se/wiki/PluginDownload. This package is
76known to work with `se.lu.onk.BaseFile` version 1.0.
77{{{
78  check out project, see instructions below
79  # cd /path/to/se.lu.onk.ReplicateError
80  # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz
81  # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz.MD5
82  # optionally compare the MD5 sum of the downloaded file and the MD5-file
83  # tar zxpf BaseFile-1.0.tgz
84  # ln -s BaseFile-1.0 BaseFile
85    or
86  # mv BaseFile-1.0 BaseFile
87}}}
88It is important that the `BaseFile` package is located in directory
89`BaseFile`. Now simple issue `ant`. This will create a jar file
90`dist/ReplicateError.jar`.
91
92
93== Creating a distribution ==
94
95Update the version number (make sure they match) in `build.xml`,
96`lib/pluginConfigurationAA.base`, and `lib/pluginConfigurationWA.base`.
97Issue `ant package`. This creates a distribution package with all
98required components, including BaseFile.jar and associated files.
99
100
101== Bug Reporting ==
102
103You can report `se.lu.onk.ReplicateError` bugs on
104
105  http://baseplugins.thep.lu.se/newticket
106
107Use user `base` and password `base`.
108
109
110== Subversion Access ==
111
112The `se.lu.onk.ReplicateError` source repository is available via anonymous
113subversion access, issue:
114
115  `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.ReplicateError/trunk se.lu.onk.ReplicateError`
116
117There is no guarantees about the contents or quality of the latest
118code in the subversion repository: it is not unheard of for code that
119is known to be broken to be committed to the repository. Use at your
120own risk. You may prefer to check out a released version instead, then
121replace `trunk` with `tags/release-number` in the above example.
122
123
124
125----------------------------------------------------------------------
126{{{
127Copyright (C) 2008 Jari Häkkinen
128
129This file is part of the se.lu.onk.ReplicateError plug-in for
130BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is
131http://base.thep.lu.se
132
133This is free software; you can redistribute it and/or modify it under
134the terms of the GNU General Public License as published by the Free
135Software Foundation; either version 3 of the License, or (at your
136option) any later version.
137
138This package is distributed in the hope that it will be useful, but
139WITHOUT ANY WARRANTY; without even the implied warranty of
140MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
141General Public License for more details.
142
143You should have received a copy of the GNU General Public License
144along with this package. If not, see <http://www.gnu.org/licenses/>.
145}}}
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