source: trunk/se/lu/thep/affymetrix/INSTALL @ 272

$Id: INSTALL 272 2007-05-21 15:57:41Z peter $

Copyright (C) 2006 Jari Häkkinen
Copyright (C) 2007 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.
----------------------------------------------------------------------
= Installation Guide for se.lu.thep.affymetrix =
This file contains installation information for two plugins: RMAExpress
and Plier.
If you think these instructions are worthless or stupid or maybe both,
please tell me and I'll try to improve them. Even better, tell me how
to improve them. My email address is jari@thep.lu.se
== 0. Introduction ==
=== Short intro: ===
The route for successful first time installation of this RMAExpress plugin is
  i. Install the plug-in.
  i. Install wxWidgets.
  i. Install RMAExpressConsole.
  i. Make BASE aware of the new plug-in.
The route for successful first time installation of this Plier plugin is
  i. Install the plug-in.
  i. Install apt-probeset-summarize.
  i. Make BASE aware of the new plug-in.
Upgrading the plug-in is even easier, see item 7) 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 plug-in for
BASE you can safely skip to item 7) below.
== 1. Pre-requisites ==
i) Pre-requisite for both all install options:
This plug-in will only work with BASE 2.0 or later, i.e. BASE 1.2.x is
not (and will never be) supported.
ii) Pre-requisite for RMAExpress plug-in (both binary package and
subversion tree installs): Installation of RMAExpressConsole.
Pre-requisite for Plier plug-in (both binary package and
subversion tree installs): Installation of apt-probeset_summarize.
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 10.2 and
MacOSX 10.4.8). Download v0.5alpha7, unpack and issue 'make'. This
will compile RMAExpressConsole and som other binaries which are of no
interest here.
apt-probeset-summarize is available in the Affymetrix Power Tools
package available through Affymetrix home page
http://www.affymetrix.com/support/developer/powertools/index.affx
You should install the binaries (RMAExpressConsole and
apt-probeset-summarize) such that it is 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.
iii) Pre-requisite for subversion tree compilation:
Compile time access to BASE core jar file.
The BASE2Core.jar (from BASE 2.0 and later) file in use by the server
running the BASE web application.
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-in:
 - Login 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
   "<base-dir>/www/plugins/se/lu/thep/affymetrix/RMAExpress.jar" in
   the 'Path' field. Replace <base-dir> with whatever you used in item
   3.v) above. 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).
5. Remember to install RMAExpressConsole according to the conditions
   stated in item 1.ii) above.
6. That's it, now you need to BASE skills to actually make use of the
   RMAExpress plug-in. Read the README file for some pointers on what
   to do now.
7. Updating RMAExpressConsole or RMAExpress plug-in for BASE.
	 a) RMAExpressConsole
	 Installing a new RMAExpressConsole binary is trivial, just replace
	 the old binary with the new binary.
	 b) RMAExpress plug-in for BASE.
	 This is straighforward:
	 - Replace the old jar-file and
	 - Login to BASE with plug-in administrative privileges.
	 - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
	 - Locate the RMAExpress plug-in 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.