source:
plugins/base1/se.lu.onk.ReplicateError/trunk/README
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$Id: README 801 2008-10-01 14:25:44Z jari $
About se.lu.onk.ReplicateError
The se.lu.onk.ReplicateError plug-in for BASE is an implementation
of 'Analysis of replicates' in Within the fold: assessing
differential expression measures and reproducibility in microarray
assays, Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062
download article.
Two algorithms are implemented, within assays (cf. figure 4 in the
publication) and across assays ((cf. figure 5 in the publication).
se.lu.onk.ReplicateError is free software. See the file license.txt for
copying conditions.
The package was created by Johan Enell and is currently maintained by Jari Häkkinen.
Downloading
se.lu.onk.ReplicateError can be obtained from
Installation and upgrade
This plug-in is only tested in BASE 2.8 through the Base1PluginExecuter but is expected to work also in BASE 1.2.17. Please report failure or success in BASE 1.2 through http://baseplugins.thep.lu.se. These installation instructions only describe how to get the plug-in to work with the Base1PluginExecuter in the latest BASE version 2. BASE 1.2 installers should enable one line in files AAtabs.html and WAtabs.html, read the information in these short files.
If you downloaded a binary package you only need to follow these instructions. If you prefer to compile the package yourself, read the instructions about compiling and creating a distribution before doing the installation steps described here.
You need to understand how to install plug-ins in BASE, please refer to BASE documentation at http://base.thep.lu.se for general instructions on plug-in installation. The BASE documentation contains a chapter on plug-ins. If you have read the plug-in information you should be able to follow this path
# cd /path/to/base/plugins # download ReplicateError-version.tgz # untar ReplicateError-version.tgz # ln -s ReplicateError-version ReplicateError
The symbolic link in the last line above allows for easier change to future version of the plug-in.
# Log in to your BASE as admin
# Upload the configuration files `pluginConfigurationAA.base` and
`pluginConfigurationWA.base`.
# Create/update one configuration each for across and within assays
mode of the ReplciateError plug-in where you select the plug-in
defintion files `pluginConfigurationAA.base` and
`pluginConfigurationWA.base`, respectively. BASE will respond that
plug-ins where configured but ...
# Re-configure the plug-ins without selecting a file, set the
`Plugin executables path` and proceed to next window by clicking
`Next`. This is explained in the BASE documentation and needs to
be done even when you update your plug-in.
# In this parameter window set the `Name of executable`. The value
of this parameter and `Plugin executables path` should add up to
the absolute path to the binaries `runAA` and `runWA`, i.e.,
/path/to/base/plugins/ReplicateError/runAA. How this string looks
like depends on your plug-in directory structure.
# Test the plug-ins and when you are satisfied, share it to your
users.
Compiling
You must checkout the se.lu.onk.ReplicateError from the repository,
follow the instructions below. Then download and untar the
se.lu.onk.BaseFile package available from
http://baseplugins.thep.lu.se/wiki/PluginDownload. This package is
known to work with se.lu.onk.BaseFile version 1.0.
check out project, see instructions below
# cd /path/to/se.lu.onk.ReplicateError
# wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw -O BaseFile-1.0.tgz
# wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz.MD5?format=raw -O BaseFile-1.0.tgz.MD5
# optionally compare the MD5 sum of the downloaded file and the MD5-file
# tar zxpf BaseFile-1.0.tgz
# ln -s BaseFile-1.0 BaseFile
or
# mv BaseFile-1.0 BaseFile
It is important that the BaseFile package is located in directory
BaseFile. Now simple issue ant. This will create a jar file
dist/ReplicateError.jar.
Creating a distribution
Update the version number in build.xml, and issue `ant
package`. This creates a distribution package with all required
components, including BaseFile?.jar and associated files.
Bug Reporting
You can report se.lu.onk.ReplicateError bugs on
Use user base and password base.
Subversion Access
The se.lu.onk.ReplicateError source repository is available via anonymous
subversion access, issue:
svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.ReplicateError/trunk se.lu.onk.ReplicateError
There is no guarantees about the contents or quality of the latest
code in the subversion repository: it is not unheard of for code that
is known to be broken to be committed to the repository. Use at your
own risk. You may prefer to check out a released version instead, then
replace trunk with tags/version in the above example.
Copyright (C) 2008 Jari Häkkinen This file is part of the se.lu.onk.ReplicateError plug-in for BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is http://base.thep.lu.se This is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package. If not, see <http://www.gnu.org/licenses/>.
