[LMS-2313] updated documentation

SVN: 21668

plasmid/resource/PlasMapper/README.txt

@@ -5,10 +5,15 @@ This directory contains:
 - PlasMapper_download.tar.gz 
 		version 2.0 of PlasMapper downloaded from http://wishart.biology.ualberta.ca/PlasMapper.
 - PlasMapper_dist.zip 
-		compressed distribution directory created in step 4 of the following instructions
+		compressed distribution directory created in step 5 of the following instruction
+- YeastLab-common_enzymes.txt
+		list of common enzymes used in Yeast Lab
+- YeastLab-PlasMapper_dist.zip (TODO)
+		distribution with common enzymes changed to the ones used in Yeast Lab
 - example.gb
 		exmple GB file that can be used for testing after installation is complete
 
+
 *Installation instructions for version 2.0*
 
 1. Unpack PlasMapper_download.tar.gz into your workspace. 
@@ -17,23 +22,26 @@ This directory contains:
 - Fix build path:
 -- remove /tmp/tomcat/common/lib/servlet-api.jar
 -- add /libraries/jetty/servlet-api-2.5.jar
-- [optional] change settings (can be done later, deployment)
+- [optional] change settings (can be done later, when deploying the application)
 -- properties file: ca.ualberta.xdong.plasMapper.annotate.plasMapConfiguration_en_CA.properties
--- change '/home/tomcat/webapps/PlasMapper' to the path where PlasMapper will be deploed
--- 'plasMapRoot' can lead to an external directory, where PlasMapper will create tmp directory
+-- change '/home/tomcat/webapps/PlasMapper' to the path where PlasMapper will be deployed
+-- 'plasMapRoot' leads to an external directory, where PlasMapper will create tmp directory
    for its output
 3. in build.xml change values of properties: 
 - <property name="installdir" value="dist"/>
 - <property name="servletjar" value="../libraries/jetty/servlet-api-2.5.jar"/>
-4. run ant install
-5. copy dist/webapps/PlasMapper to webapps of the application server 
+4. [optional] change list of common enzymes in 
+	ca.ualberta.xdong.plasMapper.annotate.PlasmidCleavageSiteAnnotate.java
+	(for Yeast Lab see YeasLab-common_enzymes.txt)
+5. run ant install
+6. copy dist/webapps/PlasMapper to webapps of the application server 
 (make sure plasMapConfiguration_en_CA.properties are properly configured)
 
 Additionally there needs to be blastall installed on the machine running PlasMapper. Latest
 version can be downloaded from ftp://ftp.ncbi.nih.gov/blast/executables/release/LATEST.
 
-Go to <server root>/PlasMapper/ after deployment to check that everything is working. You should
-be able to generate a PNG for 'example.gb' file from this directory:
+Go to http://<server root>:8080/PlasMapper/ after deployment to check that everything is working. 
+You should be able to generate a PNG for 'example.gb' file from this directory:
 - select the GB file
 - change the Image Size from 850x750 to 1200x1000
 - click on Graphic Map button (below DNA sequence text area)
\ No newline at end of file

plasmid/resource/README

@@ -6,7 +6,7 @@ h1. How to test on productive server (temporary)
 -- create/delete samples attached to EXPERIMENT_TEST (don't delete sample SAMPLE_TEST)
 -- register/delete datasets attached to test samples 
 2. Login to bs-plasmids.ethz.ch as openbis 
-3. There is a link 'dss-data' to a shared directory with e.g. a dropbox ('incoming') and an example
+3. There is a link 'dss-data' to a shared directory with a dropbox ('incoming') and an example
 of a directory with files that can be registered as datasets for sample SAMPLE_TEST.
 - to register datasets for the SAMPLE_TEST sample copy ~/dss-data/SAMPLE_TEST to ~/dss-data/incoming 
 
@@ -28,7 +28,7 @@ PlasMapper/WEB-INF/classes/ca/ualberta/xdong/plasMapper/annotate/plasMapConfigur
 - targets/playground/data/incoming
 - targets/playground/data/incoming-cifex
 - targets/playground/data/store
-3.2 change in /etc/service.properties values of properties needed for PlasMapper integration
+3.2 change values of properties in /etc/service.properties needed for PlasMapper integration
 main-thread.storage-processor.plasmapper-root-dir
 main-thread.storage-processor.plasmapper-base-url