GenePattern Goodies/Badies

GP installer fails to launch, Java throws exception:

Preparing to install...
Extracting the installation resources from the installer archive...
Configuring the installer for this system's environment...

Launching installer...

An internal LaunchAnywhere application error has occured and this application cannot proceed. (LAX)

Stack Trace:
java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
        at java.util.Properties.loadConvert(Properties.java:569)
        at java.util.Properties.load0(Properties.java:392)
        at java.util.Properties.load(Properties.java:342)
        at com.zerog.common.java.util.PropertiesUtil.loadProperties(DashoA10*..)
        at com.zerog.lax.LAX.(DashoA10*..)
        at com.zerog.lax.LAX.main(DashoA10*..)

After some googling around, I discovered that Launch Anywhere often screws around with PS1, so changing this for the current shell resolves the issue:

$ export PS1=">"

Some basic ways to access GP's HSQLDB:

You must have RC configuration file(s) in the home directory either sqltool.rc or dbmanager.rc:

# This is for a hsqldb Server running with default settings on your local
# computer (and for which you have not changed the password for "SA").
urlid gp
url jdbc:hsqldb:hsql://127.0.0.1:9001/xdb
username sa
password

Then sqltool (commandline) or DatabaseManager (GUI) can be called:

java -cp hsqldb.jar org.hsqldb.util.DatabaseManager --urlid gp

If GP is installed on NFS share, it fails to start due to the HSQLDB failure.

This is NOT GP's issue. It's a HSQLDB issue. The workaround is disble HSQLDB file locking by presenting these in DB's properties file:

pwbcad@ubuntu:data$ cat db0.properties
hsqldb.nio_data_file=false
hsqldb.lock_file=false
...

UPDATE: the above method is for version between 1.7.2. and 1.8.0. Couldn't find out which version the GP uses. But tried replace the hsqldb.jar with the 1.8.10 version, now GP can start successfully.