From ccf8749244920e163b35a773dd2e43df09e63120 Mon Sep 17 00:00:00 2001 From: Suzanne Duce Date: Thu, 3 Apr 2014 09:53:07 +0100 Subject: [PATCH] JWS-86 edited text --- website/man_configuration.html | 46 ++++++++++++++++++++-------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/website/man_configuration.html b/website/man_configuration.html index e07ffc9..8e0bb14 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -101,7 +101,7 @@ the amount of memory available for the web application server. If you are using Apache-Tomcat, then you can define its memory settings in the JAVA_OPTS environment variable. To specify which JVM to use for Apache-Tomcat, put the full path to the JRE -installation in the JAVA_HOME environment variable (We would +installation in the JAVA_HOME environment variable. (We would recommend using Sun Java Virtual Machine (JVM) in preference to Open JDK). Below is an example of code which can be added to <tomcat_dir>/bin/setenv.sh script @@ -123,7 +123,7 @@ false
cluster.tmp.directory=/homes/clustengine/testoutput- a directory to use for temporary files storage. The value must be -an absolute path to the temporary directory. Required. The value +an absolute path to the temporary directory. This is required. The value must be different from what is defined for local engine. This directory must be accessible from all cluster nodes.
For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH @@ -168,9 +168,9 @@ optional>

Default JABAWS configuration includes path to local executables to be run by the local engine only, all cluster related settings -are commented out, but they are there for you as example. Cluster +are commented out, but they are there for you as examples. Cluster engine is disabled by default. To configure executable for cluster -execution un comment the X.cluster settings and change them +execution uncomment the X.cluster settings and change them appropriately.

By default limits are set well in excess of what you may want to offer to the users outside your lab, @@ -244,7 +244,7 @@ the fasta executable, which is not supplied with Mafft, but is a separate package. Mafft needs to know the location of fasta34 executable.

-

To let Mafft know where the other files from its package are +

To let Mafft know where the other files from its package are, change the value of MAFFT-BINARIES environment variables. To let Mafft know where is the fasta34 executable set the value of FASTA_4_MAFFT environment variable to point to a location of @@ -264,7 +264,7 @@ defined in JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service for many users. By defining a maximum allowed task size you can provide an even service for all users and -prevents waist of resources on the tasks too large to complete successfully. You can define the maximum +prevents waste of resources on the tasks too large to complete successfully. You can define the maximum number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service independently. Furthermore, you can define different limits for different presets of the same web service.
@@ -274,25 +274,25 @@ files.

Using a different version of the alignment program with JABAWS

- JABAWS supplied with binaries and source code of the executables which version it supports. So normally you + JABAWS is supplied with binaries and source code of the executables related to the version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions - JABAWS executable supported. This could be the case with more recent executable. If the options supported - by your chosen executable is different when the standard JABAWS executable, than you need to edit + JABAWS executable require. This could be the case with more recent executable. If the options supported + by your chosen executable is different from the standard JABAWS executable, then you need to edit ExecutableNameParamaters.xml  configuration file.

Load balancing

- If your cluster is busy and have significant waiting times you can achieve a faster response by allowing - the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works + If your cluster is busy and has significant waiting times, you can achieve a faster response by allowing + the server machine to calculate small tasks and then reserve the cluster for bigger jobs. This works especially well if your server is a powerful machine with many CPUs. To do this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. Then, edit "# LocalEngineExecutionLimit #" preset in <ServiceName>Limits.xml file accordingly. JABAWS server then - will balance the load according to the following rule: If the task size is smaller then the maximum task - size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit + will balance the load according to the following rule: If the task size is smaller than the maximum task + size for local engine, and the local engine has idle threads, then it calculates task locally otherwise it submit the task to the cluster.

@@ -309,9 +309,9 @@ files.

Alternatively, you can use a command line client (part of the client only package) to test your JABAWS installation as described here. If you downloaded a JABAWS server package, you can use <your_jaba_context_name>/WEB-INF/lib/jaba-client.jar to test JABAWS installation as described in <your_jaba_context_name>/WEB-INF/lib/jaba-client.jar to test JABAWS installation as described here. If you downloaded the source - code, then you could run a number of test suits defined in the + code, then you could run a number of test suites defined in the build.xml Apache Ant file.

JABAWS requests logging

Enable Tomcat log valve. To do this uncomment the following section of <tomcat_root>/conf/server.xml configuration file.

@@ -336,7 +336,7 @@ files.

Which can be processed in various programs for log analysis , such as WebAlizer, Analog, AWStats.

JABAWS internal logging

-

JABAWS can be configured to log what it is doing. This comes +

JABAWS can be configured to log what it is doing. This comes in handy if you would like to see who is using your web services or need to chase some problems. JABAWS uses log4j to do the logging, @@ -344,8 +344,8 @@ files.

You will find it in the /WEB-INF/classes/log4j.properties file. All the lines in this file are commented out. The reason why the logging is - disabled by default it simple, log4j have to know the exact - location where the log files should be stored. This is not known up + disabled by default it simple, log4j has to know the exact + location of where the log files are stored. This is not known up until the deployment time. To enable the logging you need to define logDir property in the log4j.properties and uncomment section of @@ -381,16 +381,16 @@ class="hightlight">log4j.properties and uncomment section of ExecutionStatistics - The database for storing the execution statistics. + The database for storing the execution statistics statpages - Web pages for usage statistics visialization and webservices status queries. + Web pages for usage statistics visialization and webservices status queries jobsout/ Contains directories generated when running an individual executable. E.g. input and output files and some other task - related data. (optional) + related data (optional) binaries/ @@ -400,11 +400,11 @@ class="hightlight">log4j.properties and uncomment section of binaries/src Contains source of native executables and Linux i386 - binaries. + binaries binaries/windows - Contains binaries for MS Windows operating system. + Contains binaries for MS Windows operating system binaries/matrices -- 1.7.10.2