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ssadedin / bpipe

Bpipe - a tool for running and managing bioinformatics pipelines
http://docs.bpipe.org/
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GroovyStarter error #71

Open lonsbio opened 10 years ago

lonsbio commented 10 years ago

From cboust...@gmail.com on 2013-02-23T02:45:23Z

What steps will reproduce the problem? 1. Download and unzip bpipe

  1. Tried to run helloworld.pipe example from documentation (bpipe run helloworld.pipe)
  2. get the error below What is the expected output? What do you see instead? Exception in thread "main" java.lang.NoClassDefFoundError: org/codehaus/groovy/tools/GroovyStarter Caused by: java.lang.ClassNotFoundException: org.codehaus.groovy.tools.GroovyStarter at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: org.codehaus.groovy.tools.GroovyStarter. Program will exit. What version of the product are you using? On what operating system? bpipe-0.9.7.tar.gz Ubuntu 12.04 LTS Please provide any additional information below. Downloaded bpipe, tried to run the helloworld.pipe example.

Complained about Groovey not being present

Installed groovey

put GROOVEY_HOME and JAVA_HOME on path (ensuring to use java 1.6)

Still got the error

Original issue: http://code.google.com/p/bpipe/issues/detail?id=71

lonsbio commented 10 years ago

From karl.kas...@gmail.com on 2013-03-05T05:22:14Z

Hi !

This is some problem with java. You can not start bpipe from a linked file. I usually have ~/software/bin in my $PATH where i collect links of all my binaries.

This is not working with bpipe. You HAVE TO put the folder with the bpipe binary into your $PATH!

I found out the hard way, although its clearly stated here: https://code.google.com/p/bpipe/wiki/InstallInstructions

lonsbio commented 10 years ago

From cboust...@gmail.com on 2013-03-05T06:21:46Z

Hi, thanks for getting back to me.

I have tried as you suggested I have added the bpipe bin folder to my PATH

echo $PATH /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

export PATH=$PATH:/home/chris/Downloads/bpipe-0.9.8_beta_3/bin/ export PATH=$PATH:/home/chris/Downloads/jdk1.6.0_39/bin/ export PATH=$PATH:/home/chris/Downloads/groovy-1.8.9/bin/

echo $PATH /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/chris/Downloads/bpipe-0.9.8_beta_3/bin/:/home/chris/Downloads/jdk1.6.0_39/bin/:/home/chris/Downloads/groovy-1.8.9/bin/

Tried again to run bpipe bpipe run helloworld.pipe

Exception in thread "main" java.lang.NoClassDefFoundError: org/codehaus/groovy/tools/GroovyStarter Caused by: java.lang.ClassNotFoundException: org.codehaus.groovy.tools.GroovyStarter at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: org.codehaus.groovy.tools.GroovyStarter. Program will exit.

Which is the same error as before

Any more ideas, am I using the correct java version (jdk1.6.0_39)?

Thanks again for your help

lonsbio commented 10 years ago

From karl.kas...@gmail.com on 2013-03-21T14:42:51Z

what happens if you do: cd /home/chris/Downloads/bpipe-0.9.8_beta_3/bin/ ./bpipe

?

lonsbio commented 10 years ago

From calviell...@gmail.com on 2013-04-22T01:55:10Z

Same error here, executing the helloworld.pipe. Same error when executing binaries copied in the PATH and by executing the one in the bpipe-0.9.8/bin extracted folder. Using CentOs 6.4

jsolvason commented 7 years ago

I am getting same error... Has this been resolved somewhere else?