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.
- 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.
- 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.
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 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 ofGoogle Analytics can be disabled or adjusted by removing/editing conf/GA.properties Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!
All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.
-