Changeset 189 for trunk/se/lu/thep/affymetrix/INSTALL

Timestamp:

Oct 27, 2006, 10:53:18 AM (17 years ago)

Author:

Jari Häkkinen

Message:

Fixed installation problems. Changed default installation path.

File:

• trunk/se/lu/thep/affymetrix/INSTALL (modified) (8 diffs)

trunk/se/lu/thep/affymetrix/INSTALL

@@ -31 +31 @@
 0. Introduction
 
-There is two supported ways to install the RMAExpress plug-in, you
-either download a pre-compiled plug-in package (RMAExpress itself is
-not a part of this 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 two cases.
-
-Irrespective which option you choose, there may be a need to compile
-RMAExpress. This plug-in utilize an external program for the
-underlying RMA algorithm. RMAExpress must be installed for this
+There are two supported ways to install the RMAExpress plug-in, 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 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.
 
@@ -47 +48 @@
 
 Users who prefer the live on bleeding edge software and compiles the
-source from the subversion repository must go through all items below.
+source from the subversion repository must go through all items except
+3.v).
 
 If you are upgrading a previously installed RMAExpress plug-in for
@@ -55 +57 @@
 1. Pre-requisites
 
-i) Pre-requisite for both binary package and subversion tree installs:
+i) Pre-requisite for both all install options:
 This plug-in will only work with BASE 2.0 (revision 2512) or later,
 i.e. BASE 1.2.x is not (and will never be) supported.
@@ -82 +84 @@
 fulfilled, but execution of the plug-in will fail.
 
-iii) Pre-requisite for subversion tree compilation: Compile time
-access to BASE core jar file.
+iii) Pre-requisite for subversion tree compilation:
+Compile time access to BASE core jar file.
 
 The BASE2Core.jar (must be later than subversion revision 2512) file
@@ -89 +91 @@
 
 
-2. Compilation of source from the subversion repository
-
-iv) If you install from a subversion working copy you must compile the
-plug-in, do
-
-        make
+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.
-
-
-3. Installation
-
-v) Install the plug-in in the BASE application server file system. If
-BASE is installed in /usr/local/base simply do
-
-  make install
-
-If BASE is installed elsewhere, do
-
-  make BASEROOT=<base-dir> install
-
-where <base-dir> is to be replaced by the path to BASE. The plug-in
-will install in the recommended directory
-<base-dir>/plugins/se/lu/thep/affymetrix, i.e. if you prefer another
-location please refer to the Makefile (which supports further options).
+  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
@@ -131 +127 @@
 
 
+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
 
@@ -141 +167 @@
  - 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>/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.
+   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
@@ -178 +205 @@
    - 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.
+   - 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.