JABAWS MANUAL
-JABAWS Configuration
+JABAWS Server Configuration
- JABAWS Configuration
- Local Engine Configuration
- Cluster Engine Configuration
- Executable Configuration -
- Defining Environment Variables for - Executables -
- Configure JABAWS to Work -with Mafft +
- Defining Environment Variables for Executables +
- Configure JABAWS to Work with Mafft
- Limiting the size of the job accepted by JABAWS Server
- Using a different version of the alignment program with JABAWS
- Load balancing @@ -65,7 +66,7 @@ with Mafft
- JABAWS requests logging
- JABAWS internal logging
- JABAWS War File Content -
- JABAWS Usage Statistics +
- JABAWS and Google Analytics
JABAWS Configuration
There are three parts of the system you can configure. The local
@@ -100,7 +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
@@ -122,7 +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
@@ -167,11 +168,15 @@ 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, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.
+
+ By default limits are set well in excess of what you may want to offer to the users outside your lab,
+ to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000
+ letters on average for all of the JABA web services. You can adjust the limits according to your
+ needs by editing conf/settings/<X>Limit.xml files.
After you have completed the editing your configuration may look like
this:local.mafft.bin.windows=
local.mafft.bin=binaries/mafft
@@ -187,9 +192,11 @@ appropriately.
Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly -specify the absolute path to anything -normally evaluated from an environment variable at execution time.
++Furthermore, you should avoid using environment variables within the paths or options - since +these will not be evaluated correctly. Instead, please explicitly specify the absolute path +to anything normally evaluated from an environment variable at execution time. +
If you are using JABAWS to submit jobs to the cluster (with cluster engine enabled), executables must be available from all @@ -206,7 +213,7 @@ can access and execute them.
just pass whatever is specified in this line directly to the cluster submission library. This is how DRMAA itself treats this settings. More exactly DRMAA JobTemplate.setNativeSpecification() function will be called. - +For further details and examples of configuration please refer to the Executable.properties file supplied with JABAWS.
Defining Environment Variables for Executables
@@ -237,7 +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 @@ -254,20 +261,57 @@ by providing an absolute path to them. All these settings are defined in conf/Executable.properties file.
Limiting the size of the job accepted by JABAWS
-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 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.
-By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.
+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 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.
+
+By default limits are disabled. You can enable them by editing conf/Executable.properties
+file. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml
+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 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 ExecutableNameParamaters.xml configuration file.
++ 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 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 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 the task to the cluster.
++ 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 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. +
+Testing JABA Web Services
-You can use a command line client (part of the client only +
+ Access <your_JABAWS_server_URL>/ServiceStatus to test all web services. + Each time you access this URL, all services are tested. + + For production configuration we recommend prohibiting requests to this URL for non + authenticated users to prevent excessive load on the server. +
+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.
@@ -292,7 +336,7 @@ By default limits are set well in excess of what you may want to offer to the u