From 4582408e6dea3abbacb5c015a7e367182e091926 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 10 Jun 2011 13:31:11 +0000
Subject: [PATCH] [LMS-2313] updated documentation
SVN: 21668
---
plasmid/resource/PlasMapper/README.txt | 24 ++++++++++++-------
.../YeastLab-common_enzymes.txt | 0
plasmid/resource/README | 4 ++--
3 files changed, 18 insertions(+), 10 deletions(-)
rename plasmid/resource/{ => PlasMapper}/YeastLab-common_enzymes.txt (100%)
diff --git a/plasmid/resource/PlasMapper/README.txt b/plasmid/resource/PlasMapper/README.txt
index cda42dce226..b37957447ae 100644
--- a/plasmid/resource/PlasMapper/README.txt
+++ b/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
diff --git a/plasmid/resource/YeastLab-common_enzymes.txt b/plasmid/resource/PlasMapper/YeastLab-common_enzymes.txt
similarity index 100%
rename from plasmid/resource/YeastLab-common_enzymes.txt
rename to plasmid/resource/PlasMapper/YeastLab-common_enzymes.txt
diff --git a/plasmid/resource/README b/plasmid/resource/README
index 3b742d9750a..6409f9bc58d 100644
--- a/plasmid/resource/README
+++ b/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
--
GitLab