Changeset 273 for trunk/se/lu/thep/affymetrix/INSTALL

Timestamp:

May 21, 2007, 6:35:14 PM (16 years ago)

Author:

Peter Johansson

Message:

some more installation instructions for affymetrix package refs #45

File:

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

trunk/se/lu/thep/affymetrix/INSTALL

@@ -23 +23 @@
 Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
 USA.
+}}}
 ----------------------------------------------------------------------
 
@@ -124 +125 @@
 
 
-2. Compilation and installation from a subversion tree
+== 2. Compilation and installation from a subversion tree ==
 
 You should skip this section if you downloaded a pre-compiled package.
@@ -131 +132 @@
 the plug-in, do
 
-  make
-
-This assumes that BASE is installed in /usr/local/base. If this is not
+  `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
+  `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
+  `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
+`<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
+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
@@ -160 +161 @@
 
 
-3. Installation from a pre-compiled package
+== 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
+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
+  `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
+`<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
+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
@@ -190 +191 @@
 
 
-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
+== 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
@@ -205 +206 @@
    3.v) above. Click on the 'Save' button.
 
- - Share the plug-in to all users/roles/groups that should have
+ * 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.
+ * That's it, now you need to BASE skills to actually make use of the
+   plug-in. Read the README file for some pointers on what to do now.
+
+== 7. 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.
+
+=== Update RMAExpress or Plier plug-ins for BASE ===
 
    This is straighforward:
@@ -236 +234 @@
    - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
 
-   - Locate the RMAExpress plug-in in the list and click on it.
+   - 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
@@ -246 +244 @@
 
    - Done.
+