Error: Could not find or load main class org.codehaus.groovy.tools.GroovyStarter

[w8120...@gmail.com]

Hi,

I'm running JAFFA with my own data,and I got some problems.

I installed groovy ,and type groovy --version , it shows Groovy Version: 2.5.8 JVM: 1.8.0_65 Vendor: Oracle Corporation OS: Linux

Then I run the script ./install_linux64.sh as suggested and showed All commands installed successfully!

when I run /home/software/JAFFA-version-1.09/tools/bin/bpipe run /home/software/JAFFA-version-1.09/JAFFA_direct.groovy /home/data/sample01*.gz, it showed 

Error: Could not find or load main class org.codehaus.groovy.tools.GroovyStarter

I used groovy to debug: groovy -d /home/software/JAFFA-version-1.09/JAFFA_direct.groovy

    Caught: groovy.lang.MissingPropertyException: No such property: bpipe for class: JAFFA_direct

    groovy.lang.MissingPropertyException: No such property: bpipe for class: JAFFA_direct

        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:65)

        at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:51)

        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:309)

        at JAFFA_direct.run(JAFFA_direct.groovy:12)

        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:266)

        at groovy.lang.GroovyShell.run(GroovyShell.java:376)

        at groovy.lang.GroovyShell.run(GroovyShell.java:365)

        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:592)

        at groovy.ui.GroovyMain.run(GroovyMain.java:336)

        at groovy.ui.GroovyMain.access$1400(GroovyMain.java:69)

        at groovy.ui.GroovyMain$GroovyCommand.process(GroovyMain.java:295)

        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)

        at groovy.ui.GroovyMain.main(GroovyMain.java:116)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:497)

        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:110)

        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:128)

I wonder how to solve this, thanks a lot.

[Nadia Davidson]

Hi,

Sorry for the slow reply. You may have already resolved this issues, but in case not, what happens when you run /home/software/JAFFA-version-1.09/tools/bin/bpipe alone? Do you get help information or an error? 

Cheers,

Nadia

[ssad...@gmail.com]

Hi,

This might be happening because you have another / conflicting groovy version installed to what Bpipe uses internally. Something you could try is making sure that GROOVY_HOME is not set as an environment variable - ie:

unset GROOVY_HOME

Can you give that a try and see if the bpipe command works?

Cheers,

Simon