you are using Apache-Tomcat, then you can define its memory\r
settings in the JAVA_OPTS environment variable. To specify which\r
JVM to use for Apache-Tomcat, put the full path to the JRE\r
-installation in the JAVA_HOME environment variable (We would\r
+installation in the JAVA_HOME environment variable. (We would\r
recommend using Sun Java Virtual Machine (JVM) in preference to\r
Open JDK). Below is an example of code which can be added to <span\r
class="hightlight"><tomcat_dir>/bin/setenv.sh</span> script\r
<span class=\r
"hightlight">cluster.tmp.directory=/homes/clustengine/testoutput-</span>\r
a directory to use for temporary files storage. The value must be\r
-an absolute path to the temporary directory. Required. The value\r
+an absolute path to the temporary directory. This is required. The value\r
must be different from what is defined for local engine. This\r
directory must be accessible from all cluster nodes.<br />\r
For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH\r
\r
<p>Default JABAWS configuration includes path to local executables\r
to be run by the local engine only, all cluster related settings\r
-are commented out, but they are there for you as example. Cluster\r
+are commented out, but they are there for you as examples. Cluster\r
engine is disabled by default. To configure executable for cluster\r
-execution un comment the X.cluster settings and change them\r
+execution uncomment the X.cluster settings and change them\r
appropriately. </p>\r
<p>\r
By default limits are set well in excess of what you may want to offer to the users outside your lab, \r
separate package. Mafft needs to know the location of fasta34\r
executable.</p>\r
\r
-<p>To let Mafft know where the other files from its package are\r
+<p>To let Mafft know where the other files from its package are,\r
change the value of MAFFT-BINARIES environment variables. To let\r
Mafft know where is the fasta34 executable set the value of\r
FASTA_4_MAFFT environment variable to point to a location of\r
<p>\r
JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service \r
for many users. By defining a maximum allowed task size you can provide an even service for all users and \r
-prevents waist of resources on the tasks too large to complete successfully. You can define the maximum \r
+prevents waste of resources on the tasks too large to complete successfully. You can define the maximum \r
number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service \r
independently. Furthermore, you can define different limits for different presets of the same web service. \r
<br/>\r
\r
<h3><a name="diffbin" id="diffbin"></a>Using a different version of the alignment program with JABAWS</h3>\r
<p>\r
- JABAWS supplied with binaries and source code of the executables which version it supports. So normally you \r
+ JABAWS is supplied with binaries and source code of the executables related to the version it supports. So normally you \r
would not need to install your own executables. However, if you have a different version of an executable \r
(e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions \r
- JABAWS executable supported. This could be the case with more recent executable. If the options supported \r
- by your chosen executable is different when the standard JABAWS executable, than you need to edit \r
+ JABAWS executable require. This could be the case with more recent executable. If the options supported \r
+ by your chosen executable is different from the standard JABAWS executable, then you need to edit \r
<em>ExecutableName</em>Paramaters.xml configuration file.\r
</p>\r
\r
<h3><a name="mixuse" id="mixuse"></a>Load balancing </h3>\r
<p>\r
- If your cluster is busy and have significant waiting times you can achieve a faster response by allowing \r
- the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works \r
+ If your cluster is busy and has significant waiting times, you can achieve a faster response by allowing \r
+ the server machine to calculate small tasks and then reserve the cluster for bigger jobs. This works \r
especially well if your server is a powerful machine with many CPUs. To do this you need to enable and \r
configure both the cluster and the local engines. Once this is done decide on the maximum size of a task \r
to be run on the server locally. Then, edit \r
<span class="hightlight">"# LocalEngineExecutionLimit #" </span>preset \r
in <span class="hightlight"> <ServiceName>Limits.xml</span> file accordingly. JABAWS server then \r
- will balance the load according to the following rule: If the task size is smaller then the maximum task \r
- size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit \r
+ will balance the load according to the following rule: If the task size is smaller than the maximum task \r
+ size for local engine, and the local engine has idle threads, then it calculates task locally otherwise it submit \r
the task to the cluster.\r
</p>\r
\r
<p>Alternatively, you can use a command line client (part of the client only\r
package) to test your JABAWS installation as described <a href="man_client.html">here</a>. If you downloaded a JABAWS\r
server package, you can use <span class=\r
-"hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span> to test JABAWS installation as described in <a href=\r
+"hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span> to test JABAWS installation as described <a href=\r
"man_serverwar.html#usingWsTester">here</a>. If you downloaded the source\r
- code, then you could run a number of test suits defined in the\r
+ code, then you could run a number of test suites defined in the\r
build.xml Apache Ant file.</p>\r
<h3><a name="logs" id="logs"></a>JABAWS requests logging </h3>\r
<p>Enable Tomcat log valve. To do this uncomment the following section of <span class="hightlight"><tomcat_root>/conf/server.xml</span> configuration file. </p>\r
</table>\r
<p>Which can be processed in various programs for log analysis , such as <a href="http://www.webalizer.org/">WebAlizer</a>, <a href="http://www.analog.cx/">Analog</a>, <a href="http://awstats.sourceforge.net/">AWStats</a>. </p>\r
<h3><a name="logfiles" id="logfiles"></a>JABAWS internal logging </h3>\r
-<p>JABAWS can be configured to log what it is doing. This comes\r
+<p>JABAWS can be configured to log what it is doing. This comes in\r
handy if you would like to see who is using your web services or\r
need to chase some problems. JABAWS uses <a href=\r
"http://logging.apache.org/log4j/1.2/">log4j</a> to do the logging,\r
You will find it in the <span class=\r
"hightlight">/WEB-INF/classes/log4j.properties</span> file. All the\r
lines in this file are commented out. The reason why the logging is\r
- disabled by default it simple, log4j have to know the exact\r
- location where the log files should be stored. This is not known up\r
+ disabled by default it simple, log4j has to know the exact\r
+ location of where the log files are stored. This is not known up\r
until the deployment time. To enable the logging you need to\r
define<span class="hightlight"> logDir</span> property in the <span\r
class="hightlight">log4j.properties</span> and uncomment section of\r
</tr>\r
<tr>\r
<td>ExecutionStatistics</td>\r
- <td>The database for storing the execution statistics. </td>\r
+ <td>The database for storing the execution statistics </td>\r
</tr>\r
<tr>\r
<td>statpages</td>\r
- <td>Web pages for usage statistics visialization and webservices status queries. </td>\r
+ <td>Web pages for usage statistics visialization and webservices status queries </td>\r
</tr>\r
<tr>\r
<td>jobsout/</td>\r
<td>Contains directories generated when running an individual executable. E.g. input and output files and some other task\r
- related data. (optional)</td>\r
+ related data (optional)</td>\r
</tr>\r
<tr>\r
<td>binaries/</td>\r
<tr>\r
<td>binaries/src</td>\r
<td>Contains source of native executables and Linux i386\r
- binaries.</td>\r
+ binaries</td>\r
</tr>\r
<tr>\r
<td>binaries/windows</td>\r
- <td>Contains binaries for MS Windows operating system. </td>\r
+ <td>Contains binaries for MS Windows operating system </td>\r
</tr>\r
<tr>\r
<td>binaries/matrices</td>\r
git://source.jalview.org / jabaws.git / commitdiff