$Id: INSTALL 295 2007-05-23 12:40:10Z jari $

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Copyright (C) 2006 Jari Häkkinen
Copyright (C) 2007 Jari Häkkinen, Peter Johansson
This file is part of se.lu.thep.affymetrix package for BASE,
http://baseplugins.thep.lu.se/wiki/se.thep.lu.se.affymetrix
se.lu.thep.affymetrix package for BASE 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 2 of the License, or (at your option) any later version.
se.lu.thep.affymetrix package for BASE 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 program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
USA.

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Installation Guide for se.lu.thep.affymetrix

This file contains installation information for two plug-ins: RMAExpress and Plier.

0. Introduction

Short intro:

The route for successful first time installation of this RMAExpress plug-in is

1. Install the plug-in.
2. Install wxWidgets.
3. Install RMAExpressConsole.
4. Make BASE aware of the new plug-in.

The route for successful first time installation of this Plier plug-in is

1. Install the plug-in.
2. Install apt-probeset-summarize.
3. Make BASE aware of the new plug-in.

Upgrading the plug-in is even easier, see item 5) below.

Longer intro:

There are two supported ways to install this Affymetrix package, you either download a pre-compiled package or you checkout the latest source from the subversion repository. The below instructions covers both installation options since major parts of the installation is the same for the different cases. There is also a source package available for download but installation from that package is currently not supported, it is supplied for reference only.

Note, the underlying algorithms RMA and Plier are not part of this package. This package contains the plug-in code needed for hooking up RMAExpress and Plier to BASE as a plug-in. The underlying binaries, RMAExpress and Plier, must be installed for the corresponding plug-in to work. See more in item 1.ii below.

Users who prefer the install from pre-compiled packages must go through all items below except 1.iii) and 2.iv).

Users who prefer the live on bleeding edge software and compiles the source from the subversion repository must go through all items except 3.v).

If you are upgrading a previously installed RMAExpress or Plier plug-in for BASE you can safely skip to item 5) below.

1. Pre-requisites

BASE 2

This plug-in package will only work with BASE 2.0 or later, i.e. BASE 1.2.x is not (and will never be) supported.

RMAExpressConsole and apt-probeset-summarize

RMAExpressConsole

Pre-requisite for RMAExpress plug-in (both binary package and subversion tree installs) is that RMAExpressConsole is installed.

RMAExpressConsole is available in the RMAExpress package written by Ben Bolstad, and the official RMAExpress web site is ​http://rmaexpress.bmbolstad.com/

You must download and compile RMAExpressConsole. This requires that wxWidgets (a.k.a. wxWindows) is installed on your system. wxWidgets is found at ​http://www.wxwidgets.org. The compilation of RMAExpressConsole is straightforward (at least on OpenSuSE 10.0 and 10.2, and MacOSX 10.4.9). Download the source for v1.0beta1 and unpack the tar file. Unfortunately the source will not work out of the box in some operating systems. You have to add

#include <cmath>

to RawDataVisualize.cpp before issuing 'make'. After this patch RMAExpressConsole will be compiled (together with some other binaries which are of no interest here.

apt-probeset-summarize

Pre-requisite for Plier plug-in (both binary package and subversion tree installs) is that apt-probeset_summarize is installed.

apt-probeset-summarize is available in the Affymetrix Power Tools (APT) package available through Affymetrix home page ​http://www.affymetrix.com/support/developer/powertools/index.affx

APT is available as a Windows installer package and pre-built binaries for Linux and Mac OS-X. If you prefer building yourself, the source code is available as well. Though, it should be noted, we have experienced some problems building APT and at the time being we have not succeeded.

Installation of binaries

You should install the binaries (RMAExpressConsole and apt-probeset-summarize) such that they are readable for the user running your BASE application server. The name of the binaries MUST be RMAExpressConsole and apt-probeset-summarize, respectively. Also binaries must be copied into the same directory as the plug-in (see item 3.v below). These two conditions are hard coded in the plug-ins.

Install of the BASE plug-in will succeed even if this requisite is not fulfilled, but execution of the plug-in within BASE will fail.

Compile time access to BASE core jar file.

This is only needed for compilation and installation from a subversion tree, i.e., it is not needed when installing a pre-compiled package.

The BASE2Core.jar (from BASE 2.0 and later) file in use by the server running the BASE web application must be available when compiling se.lu.thep.affymetrix.jar.

2. Compilation and installation from a subversion tree

You should skip this section if you downloaded a pre-compiled package.

iv) When installing from a subversion working copy you must compile the plug-in, do

make

This assumes that BASE is installed in /usr/local/base. If this is not the case do

make BASEROOT=<base-dir>

where <base-dir> is to be replaced with the path to BASE. When the compilation finishes you install the plug-in into the BASE application server file system with

make install or make BASEROOT=<base-dir> install

The plug-in will install in the recommended directory <base-dir>/www/plugins/se/lu/thep/affymetrix, i.e., if you prefer another location please refer to the Makefile (which supports further options).

For advanced users only: <base-dir> can really be any directory readable for the user running your tomcat server. This may be handy if you run several servers on one machine but only want one common directory hierarchy for the plug-ins. Or, if you update the BASE application frequently and in the process create new directories for the newer application. More information about this is available in the Makefile.

Remember the plug-in location for configuration of BASE below.

3. Installation from a pre-compiled package

You should skip this section if you use the subversion repository.

v) Install the plug-in in the BASE application server file system. If BASE is installed in /usr/local/base simply do

make install-precompiled

If BASE is installed elsewhere, do

make BASEROOT=<base-dir> install-precompiled

where <base-dir> is to be replaced by the path to BASE. The plug-in will install in the recommended directory <base-dir>/www/plugins/se/lu/thep/affymetrix, i.e., if you prefer another location please refer to the Makefile (which supports further options).

For advanced users only: <base-dir> can really be any directory readable for the user running your tomcat server. This may be handy if you run several servers on one machine but only want one common directory hierarchy for the plug-ins. Or, if you update the BASE application frequently and in the process create new directories for the newer application. More information about this is available in the Makefile.

Remember the plug-in location for configuration of BASE below.

4. BASE configuration

vi) Make BASE aware of the new plug-ins

You need to perform the below steps for both plug-ins in this package. Currently there is no way to install all plug-ins in one package.

• Log in to BASE with plug-in administrative privileges.

• Choose 'Administrate' -> 'Plugins' -> 'Definitions'.

• Click on 'New...'. This will open up the 'Create plugin' pop-up window. Type se.lu.thep.affymetrix.RMAExpress in the 'Class' field and `/path/to/base/www/plugins/se/lu/thep/affymetrix/affymetrix.jar" in the 'Path' field. Obviously, if you have chosen another location for the jar above you should adapt to that. Click on the 'Save' button.

• Share the plug-in to all users/roles/groups that should have access to it (sharing it to group 'Everyone' should be sufficient in most cases).

• Redo the third and fourth step above for Plier where you use se.lu.thep.affymetrix.Plier in the class field.

• That's it, now you need to BASE skills to actually make use of the plug-in.

5. Updating a plug-in in BASE.

You may update the underlying binaries (RMAExpress or apt-probeset-summarize) or the plug-in.

Updating RMAExpressConsole or apt-probeset-summarize

Installing a new binary is trivial, just replace the old binary with the new binary. However, make sure that the input and output formats has not changed.

Update RMAExpress or Plier plug-ins for BASE

This is straightforward:

• Replace the old jar-file and

• Log in to BASE with plug-in administrative privileges.

• Choose 'Administrate' -> 'Plugins' -> 'Definitions'.

• Locate the plug-in (RMAExpress or Plier) in the list and click on it.

• Click on the 'Unload' button if it is available. This will remove the old plug-in from the application.

• Click on 'Edit...'. This will open up the 'Edit plugin' pop-up window. No parameter changes are need, just click on the 'Save' button.

• Done.