source: plugins/base1/

Last change on this file was 2126, checked in by Jari Häkkinen, 8 years ago

Fixes #301. Added formula information and some minor updates.

  • Property svn:eol-style set to native
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File size: 5.7 KB

$Id: README 2126 2013-11-08 15:43:09Z jari $


The plug-in is a program that creates a virtual array design for bioassays. A consequence is that the position number of each spot is changed to a negative value. The new positions are a descending integer sequence starting from -1. is open source software. See the file license.txt for copying conditions.

The package was created by Johan Enell.

Downloading can be obtained from

Installation and upgrade

This plug-in is only tested in BASE through the Base1PluginExecuter and may work also in BASE 1.2.17. Please report failure or success in BASE 1.2 through These installation instructions only describe how to get the plug-in to work with the Base1PluginExecuter in the latest BASE version 3.2.x version.

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 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 VirtualArray-version.tgz
  # untar VirtualArray-version.tgz
  # ln -s VirtualArray-version VirtualArray

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 file lib/pluginVirtualArray.base`
  # Create/update a configuration for the plug-in where you select the
    plug-in definition file `pluginVirtualArray.base`. BASE
    will respond that plug-ins where configured but ...
  # Re-configure the plug-in 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 binary `run`, i.e.,
    /path/to/base/plugins/VirtualArray/run. How this string looks
    like depends on your plug-in directory structure.
  # Create a formula (not needed when you upgrade):
    - Go to View -> Formulas page and click on the New button.
    - In the popup window enter the following information:
        Name: reporter
        Expressions: rep('id')
        Value type: Integer
        Avg. method: None
        // All other parameters can be left at their default values.
     - Save.
  # Test the plug-in and when you are satisfied, share the plug-in and
	  formula to your users.


You must checkout the from the repository, follow the instructions below. Then download and untar the package available from This package is known to work with version 1.0.

  check out project, see instructions below
  # cd /path/to/
  # wget -O BaseFile-1.0.tgz
  # wget -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
  # 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/VirtualArray.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 bugs on

Use user base and password base.

Subversion Access

The source repository is available via anonymous subversion access, issue:

svn co

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, 2009, 2013 Jari Häkkinen
This file is part of the plug-in for
BASE. Available at and BASE web site is
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
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 <>.
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