dasmoth / batman Goto Github PK

Upon installation, according to the manual in docs, I have encountered an error when I ran ant:
BUILD FAILED
[...]/batman-master/build.xml:127: [...]/batman-master/resources not found.
where [...] is the local folder where I extracted the zipped batman.
Is this directory missing (were there any essential files in there?) or it just had to be created? I have manually created it and then the build was successful. The webpage quotes in the Nature paper is not accessible anymore.

Hi
Firstly thank you for developing this tool.
I was trying to use Batman to analyze Agilent 1x244k methylation microarray but I encountered some problems of performing batman commands.
According to the manual, I've installed batman and mysql and connector/J. (I manually added a directory named "resources".)

_init:
[echo] Building batman-0.1

prepare:

prepare-java:

compile-java:
[javac] /home/lushen/batman/build.xml:118: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds

package-java:

all:

BUILD SUCCESSFUL
Total time: 0 seconds_

After that I set the classpath of all .jar files.

Then according to the manual, I tried to run batman commands but failed, such as:

lushen@biox_vm1:~/batman$ java batman.Tool -dbURL jdbc:mysql://database-server/batman_test
Error: Could not find or load main class batman.Tool
Caused by: java.lang.ClassNotFoundException: batman.Tool

lushen@biox_vm1:~/batman$ java batman.AddExpt -expt SP1A -array 12345 -tissue Sperm -sample SP1 -cy3 IP -cy5 INPUT
Error: Main method is not static in class batman.AddExpt, please define the main method as:
public static void main(String[] args)

So is there a new version of manual book for using this tool? Or could you give me some instructions?

Looking forward to your reply.