Changeset 272 for trunk/se/lu/thep/affymetrix/INSTALL

Timestamp:

May 21, 2007, 5:57:41 PM (16 years ago)

Author:

Peter Johansson

Message:

intermediate commit of new installation instructions for affymetrix package refs #45

File:

• trunk/se/lu/thep/affymetrix/INSTALL (modified) (6 diffs, 1 prop)

trunk/se/lu/thep/affymetrix/INSTALL

@@ -1 +1 @@
 $Id$
 
-======================================================================
+----------------------------------------------------------------------
+{{{
 Copyright (C) 2006 Jari Häkkinen
-
-This file is part of RMAExpress plug-in for BASE,
-http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress
-
-RMAExpress plug-in 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.
-
-RMAExpress plug-in 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.
+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
@@ -21 +23 @@
 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,
@@ -28 +35 @@
 to improve them. My email address is jari@thep.lu.se
 
-
-0. Introduction
-
-Short intro:
-
-The route for successful first time installation of this plug-in is
-a) Install the plug-in.
-b) Install wxWidgets.
-c) Install RMAExpressConsole.
-d) Make BASE aware of the new plug-in.
+== 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 the RMAExpress plug-in, you
+=== 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
@@ -51 +62 @@
 supported, it is supplied for reference only.
 
-Note, the underlying RMAExpress algorithm itself is not a part of this
-package. This packages contains the plug-in code needed for hooking up
-RMAExpress to BASE as a plug-in. RMAExpress must be installed for this
-plug-in to work, see more in item 1.ii) below.
+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
@@ -67 +79 @@
 
 
-1. Pre-requisites
-
-i) Pre-requisite for both all install options:
+== 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 both binary package and subversion tree
-installs: Installation of RMAExpressConsole.
-
-RMAExpressConsole available in the RMAExpress package written by Ben
-Bolstad, and the official RMAExpress web site is
+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/
 
@@ -88 +103 @@
 interest here.
 
-You should install the RMAExpressConsole binary such that it is
-readable for the user running your BASE application server. The name
-of the binary MUST be 'RMAExpressConsole' and copied into the same
-directory as the plug-in (see item 3.v below). These two conditions
-are hard coded in the plug-in.
+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