Using Threads in Java

The way threads work in Java is that there has to be a class implementing either Runnable interface of extends Thread class. Either way, run method must be overridden wihh desired functionality. From the client class, a new thread must be created (as below) where the first argument passed is an an instance of the class you want executed as a separate thread. Once this is done, the thread can be started by invoking start method.

Thread thrd = new Thread(new ClassImplementingThreadFunc(param1,param2));
Thread thrd2 = new Thread(new ClassImplementingThreadFunc(newParam1,newParam2));
thrd.start();
thrd2.start();

Dynamic BLAST installation and execution requirements (v0.6)

Dynamic BLAST (v0.6)

Required libraries (these must be specified in CLASSPATH)
drmaa.jar (located in $dBLAST_LOCATION/lib)
JSAP-21.jar (located in $dBLAST_LOCATION/lib)
mysql-connector-java-5.0.7-bin.jar (located in $dBLAST_LOCATION/lib)

Required source files (package com.dBLAST.util)
DynamicBLAST_6.java
ReadProperties.java

Properties files
propsLS.properties
analysis.properties
[props.properties] (pre-configured properties file for BLAST runs)

External applications/scripts
analyze.pl
runCat.pl
runGWHOST.pl
querySplittingOnly_v2.pl

Input files
first100.fas


Compiling the application
While in base directory (e.g., /home/afgane/dBLAST), execute:
javac -d bin/ src/com/dBLAST/util/*.java
(-d option specifies where to store class files. It will create all the package subdirectories from the specified folder (e.g., by specifying bin/, it will
create bin/com/dBLAST/util/ and put all class files there))
There is also a compile.sh script that automates above process.

Invoking the application
Must first execute (if not provided in .bashrc):
export dBLAST_LOCATION=/home/afgane/dBLAST
export CLASSPATH=$dBLAST_LOCATION/bin/:$dBLAST_LOCATION/lib/JSAP-2.1.jar:$CLASSPATH
Usage: java com.dBLAST.util.DynamicBLAST_6 [(-p|--propertiesFile) ] [-g|--modeGrid] [(-q|--queryFile) ] [(-d|--database) ] [-f ] [-c|--clean] [-h|--help]

[(-p|--propertiesFile) ]
Propeties file provding job arguments and options. (default:
propsLS.properties)

[-g|--modeGrid]
If switch present, analysis and fragmentation are performed on GRID
resources rather than using LOCAL resource.

[(-q|--queryFile) ]
Query input file to be used for the job (if another value is present in
the job properties file, value associated with this switch overrides
it).

[(-d|--database) ]
Query input file to be used for the job (if another value is present in
the job properties file, value associated with this switch overrides
it).

[-f ]
Defines number of fragments to be created. Once created, they are
randomly distributed to chose resources.

[-c|--clean]
Clean temporary files (most of them).

[-h|--help]
Displays this help.