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There are three parts of the system you can configure. The local and the cluster engines, and the paths to the individual executables for each engine. These settings are stored in configuration files within the web application directory (for an overview, then take a look at the war file content table).
Initially, JABAWS is configured with only the local engine enabled, with job output written to directory called "jobsout" within the web application itself. This means that JABAWS will work out of the box, but may not be suitable for serving a whole lab or a university.
The Local execution engine configuration is defined in the
properties file
If the local engine going to be heavily loaded (which is often the case if
you do not have a cluster) it is a good idea to increase
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
recommend using Sun Java Virtual Machine (JVM) in preference to
Open JDK). Below is an example of code which can be added to
export JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/
export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"
Supported configuration settings:
For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH environment variables have to be defined. They tell the cluster engine where to find DRMAA libraries. These variables should be defined when the web application server starts up, e.g.
SGE_ROOT=/gridware/sge
LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64
Finally, do not forget to configure executables for the cluster execution, they may be the same as for the local execution but may be different. Please refer to the executable configuration section for further details.
All the executable programs
are configured in
local.X.bin.windows=<path to executable under windows system, optional>
local.X.bin=<path to the executable under non-windows system, optional>
cluster.X.bin=<path to the executable on the cluster, all cluster nodes must see it, optional>
X.bin.env=<semicolon separated list of environment variables for executable, use hash symbol as name value separator, optional>
X.--aamatrix.path=<path to the directory containing substitution matrices, optional>
X.presets.file=<path to the preset configuration file, optional>
X.parameters.file=<path to the parameters configuration file, optional>
X.limits.file=<path to the limits configuration file, optional>
X.cluster.settings=<list of the cluster specific options, optional>
Where X any of the bioinformatics tools available (e.g. clustalw, muscle, mafft, probcons, t-coffee, etc.).
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 examples. Cluster engine is disabled by default. To configure executable for cluster 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
After you have completed the editing your configuration may look like
this:
local.mafft.bin=binaries/mafft
cluster.mafft.bin=/homes/cengine/mafft
mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;
mafft.--aamatrix.path=binaries/matrices
mafft.presets.file=conf/settings/MafftPresets.xml
mafft.parameters.file=conf/settings/MafftParameters.xml
mafft.limits.file=conf/settings/MafftLimits.xml
mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
Please not that relative paths must only be specified for the files that reside inside web application directory, all other paths must be supplied as absolute!
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
cluster nodes the task can be sent to, also paths to the
executables on the cluster e.g.
Executables can be located anywhere in your system, they do not have to reside on the server as long as the web application server can access and execute them.
Cluster settings are treated as a black box, the system will
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
For further details and examples of configuration please refer to the
Environment variables can be defined in property
x.bin.env
Where
mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;
The example above defines two environment variables with names MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft and /bin/fasta34 respectively. Semicolon is used as a separator between different environment variables whereas hash is used as a separator for name and value of the variable.
If you use default configuration you do not need to read any further. The default configuration will work for you without any changes, however, if you want to install Mafft yourself then there is a couple of more steps to do.
Mafft executable needs to know the location of other files supplied with Mafft. In addition some Mafft functions depends on 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,
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
fasta34 program. The latter can be added to the PATH variable
instead. If you are using executables supplied with JABAWS, the
path to Mafft binaries would be like
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
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
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
Access
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
Enable Tomcat log valve. To do this uncomment the following section of
<Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
prefix="localhost_access_log." suffix=".txt" pattern="common" resolveHosts="false"/>
The following information will be logged:
Remote IP | Date | Method server_URL protocol | HTTP status | Response size in bytes |
---|---|---|---|---|
10.31.11.159 | [10/Feb/2010:16:51:32 +0000] | "POST /jws2/MafftWS HTTP/1.1" | 200 | 2067 |
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 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,
the example of log4j configuration is bundled with JABAWS war file.
You will find it in the
After you have done this, assuming that you did not change the
log4j.properties file yourself, you should see the application log
file called
If you would like to know who is using your services, you might want to enable Tomcat request logging.
Directory | Content description |
---|---|
conf/ | contains configuration files such as Executable.properties, Engine.local.properties, Engine.cluster.properties |
conf/settings | Contains individual executable description files. In particular XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the name of the executable |
ExecutionStatistics | The database for storing the execution statistics |
statpages | 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) |
binaries/ | Directory contains native executables - programs, windows binaries (optional) |
binaries/src | Contains source of native executables and Linux i386 binaries |
binaries/windows | Contains binaries for MS Windows operating system |
binaries/matrices | Substitution matrices |
WEB-INF | Web application descriptor |
WEB-INF/lib | Web application libraries |
WEB-INF/classes | log4j.properties - log configuration file (optional) |
static | Static content such as CSS, JavaScript and Image files |
Help Pages | |
/ | help pages, index.html is the starting page |
dm_javadoc | JavaDoc for the JABAWS Data Model |
full_javadoc | JavaDoc for the complete JABAWS |
prog_docs | Documentation for programs that are included in JABAWS |
JABAWS reports web services usage to our group Google Analytics (GA) account. JABAWS usage statistics are collected for funding and reporting purposes, and no private information is collected. The data sent by JABAWS is as follows:
Google Analytics can be disabled or adjusted by removing/editing
All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.