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ssadedin / bpipe

Bpipe - a tool for running and managing bioinformatics pipelines
http://docs.bpipe.org/
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error with groovy #197

Open maojn opened 7 years ago

maojn commented 7 years ago

Hi,

I run into the following error while testing bpipe.

$ echo $PATH /usr/local/apps/bpipe/0.9.9.2/bin:/usr/local/apps/parpipe/current/scripts:/usr/local/Anaconda/envs/py2.7/bin:/usr/local/bin:/usr/local/mysql/bin:/usr/X11R6/bin:/usr/local/jdk/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/bin:/usr/bin:/usr/X11R6/bin:/home/maoj/bin:/home/maoj/bin $pwd /usr/local/apps/bpipe/0.9.9.2/bin $ ./bpipe run ../helloworld.pipe java.lang.ClassNotFoundException: bpipe.Runner at org.codehaus.groovy.tools.RootLoader.findClass(RootLoader.java:179) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:151) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:99) at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)

Any help is appreciated. Thank you.

ssadedin commented 7 years ago

The class it is looking for (bpipe.Runner) should be found in /usr/local/apps/bpipe/0.9.9.2/lib/bpipe.jar - can you check that file exists?

NB: If you just cloned your install out of Github then you need to build first (not if you downloaded the release tar.gz).