Changes between Version 15 and Version 16 of GIR4.1_NetKarma

Timestamp:

04/10/12 10:30:56 (12 years ago)

Author:

lnevers@bbn.com

Comment:

--

GIR4.1_NetKarma

@@ -12 +12 @@
 = !NetKarma How-to =
 
-0. Using the [http://d2i.indiana.edu/sites/default/files/netkarma_version2.5.1_quick_start_guide.pdf Quick Start Guide for version 2.5.1]  followed to install the Cytoscape visualization tool, the NetKarma Adaptor, and the NetKarma plug-ins for Cytoscape.
 
-1. Quick Start Guide instructs to download the Cytoscape visualization tool version 2.8.1 or later from  http://www.cytoscape.org. Downloaded Cytoscape version 2.8.2 and installed it.
+Using the [http://d2i.indiana.edu/sites/default/files/netkarma_version2.5.1_quick_start_guide.pdf Quick Start Guide for version 2.5.1]  followed to install the Cytoscape visualization tool, the NetKarma Adaptor, and the NetKarma plug-ins for Cytoscape.
 
-2: Download, build, and configure version 2.5.1 of the NetKarma Adaptor available at: http://d2i.indiana.edu/sites/default/files/karma-adaptor-2.5.1.tar.gz.  As suggested, also download NetKarma Adaptor user manual for instructions on building the Adaptor:
+Quick Start Guide provides 5 steps to follow for installation which are captured below:
+
+'''Step 1:''' Download and install the current version (2.8.1 or later) of the third-party Cytoscape visualization tool from http://www.cytoscape.org. Downloaded Cytoscape version 2.8.2 and installed it.
+
+'''Step 2:''' Download, build, and configure version 2.5.1 of the NetKarma Adaptor available at: http://d2i.indiana.edu/sites/default/files/karma-adaptor-2.5.1.tar.gz.  As suggested, also download NetKarma Adaptor user manual for instructions on building the Adaptor:
 {{{
   $ wget http://d2i.indiana.edu/sites/default/files/netkarma-gush-adaptor_v2.5_user_manual.pdf
@@ -33 +36 @@
 Had to install ant package. Need to configure "Karma-Adaptor/config/karma-adaptor.properties" not sure how to fill values yet." Built the adaptor:
 {{{
-lnevers@arendia:~/netkarma/Karma-Adaptor$ ant karma-adaptor
+$ ant karma-adaptor
 Buildfile: build.xml
 
@@ -52 +55 @@
 }}}
 
+Requested username and password for Karma-Adaptor/config/karma- adaptor.properties file.
+Attempts to use pre-existing guest account results in authentication failure.
 
+'''Step 3:''' Download the NetKarma Cytoscape Version 1.2.1 Plug-ins available at:
+
+ $ wget http://d2i.indiana.edu/sites/default/files/netkarma_visualization_plugin-1.2.1.tar.gz
+ $ tar xvzf netkarma_visualization_plugin-1.2.1.tar.gz 
+ $ cp visualization/Karma_query/KarmaRetrieval.jar cytoscape-2.8.2/plugins/.
+ $ cp visualization/Karma_query/lib/* cytoscape-2.8.2/plugins/.
+ $ cp visualization/OPM_visualization/KarmaGraph.jar cytoscape-2.8.2/plugins/.
+ $ cp visualization/OPM_visualization/lib/* cytoscape-2.8.2/plugins/.
+ $ mkdir cytoscape-2.8.2/plugins/config
+ $ cp visualization/Karma_query/config/* cytoscape-2.8.2/plugins/config/.
+ $ cp visualization/OPM_visualization/config/* cytoscape-2.8.2/plugins/config/.
+ $ cd cytoscape-2.8.2/plugins/config/
+ $ egrep "username|password" *
+
+Requested password for cytoscape-2.8.2/plugins/config files karmaQueryConfig.txt 
+and karmaVisConfig.txt and for 
 
 TO DO: