Changeset 282 for trunk/se/lu/thep/affymetrix/INSTALL

Timestamp:

May 22, 2007, 1:45:15 PM (16 years ago)

Author:

Jari Häkkinen

Message:

Improved text.

File:

• trunk/se/lu/thep/affymetrix/INSTALL (modified) (9 diffs)

trunk/se/lu/thep/affymetrix/INSTALL

@@ -83 +83 @@
 
 === RMAExpressConsole and apt-probeset-summarize === 
+
+''RMAExpressConsole''
+
 Pre-requisite for RMAExpress plug-in (both binary package and
 subversion tree installs) is that RMAExpressConsole is installed.
-
-Pre-requisite for Plier plug-in (both binary package and
-subversion tree installs) is that apt-probeset_summarize is installed.
 
 RMAExpressConsole is available in the RMAExpress package written by
@@ -96 +96 @@
 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
+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
@@ -103 +104 @@
 #include <cmath>
 }}}
-to `!RawDataVisualize.cpp' before issuing 'make'. After this patch
+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
@@ -116 +122 @@
 experienced some problems building APT and at the time being we have
 not succeeded.
+
+''Installation of binaries''
 
 You should install the binaries (RMAExpressConsole and
@@ -128 +136 @@
 
 === Compile time access to BASE core jar file. ===
+
 This is only needed for compilation and installition from a subversion
 tree, i.e., it is not needed when installing a pre-compiled package. 
@@ -203 +212 @@
 == 4. BASE configuration ==
 
-=== vi) Make BASE aware of the new plug-in ===
+=== 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.
 
  * Login to BASE with plug-in administrative privileges.
@@ -210 +223 @@
 
  * Click on 'New...'. This will open up the 'Create plugin' pop-up
-   window. Type "se.lu.thep.affymetrix.RMAExpress" in the 'Class'
+   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).
-
+   `/path/to/base/www/plugins/se/lu/thep/affymetrix/affymetrix.jar" in
+   the 'Path' field. Obviously, if you have choosen 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.
 
  * 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.
+   plug-in.
 
 == 5. Updating a plug-in in BASE. ==
@@ -232 +247 @@
 
 Installing a new binary is trivial, just replace the old binary with
-the new binary.
+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 straighforward:
+This is straighforward:
 
    - Replace the old jar-file and
@@ -244 +260 @@
    - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
 
-   - Locate the plug-in (RMAExpress or PLier) 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