source: plugins/base1/se.lu.onk.VirtualArray/trunk/README

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
  • Property svn:keywords set to Id
  • Property svn:mime-type set to text/x-trac-wiki
File size: 5.7 KB

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

About se.lu.onk.VirtualArray

The se.lu.onk.VirtualArray 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.

se.lu.onk.VirtualArray is open source software. See the file license.txt for copying conditions.

The package was created by Johan Enell.

Downloading

se.lu.onk.VirtualArray can be obtained from

http://baseplugins.thep.lu.se/wiki/PluginDownload

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 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 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 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 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.

Compiling

You must checkout the se.lu.onk.VirtualArray 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.VirtualArray
  # 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/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 se.lu.onk.VirtualArray bugs on

http://baseplugins.thep.lu.se/newticket

Use user base and password base.

Subversion Access

The se.lu.onk.VirtualArray source repository is available via anonymous subversion access, issue:

svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.VirtualArray/trunk se.lu.onk.VirtualArray

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 se.lu.onk.VirtualArray 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/>.
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