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stjude / XenoCP

A cloud-based tool for mouse read cleansing in xenograft samples
Apache License 2.0
5 stars 3 forks source link

Error: Could not find or load main class org.stjude.compbio.sam.TweakSam #11

Closed lentaing closed 4 years ago

lentaing commented 4 years ago

Hi,

I'm getting a class not found error when trying to run xenoCP. My current CLASSPATH is set to: CLASSPATH=[xenoCP install directory]/build/install/xenocp/lib:.

Can you help me locate this class? Is my CLASSPATH set correctly?

Regards, Len Taing

lentaing commented 4 years ago

UPDATE: I found that java.sh was not properly handling the CLASSPATH environment variable. I had to fix it by hard-coding my CLASSPATH into java.sh before the case statements.

adthrasher commented 4 years ago

I believe the correct CLASSPATH setting would be: CLASSPATH=[xenoCP install directory]/build/install/xenocp/lib/*:.

The directory contains JAR files, so the wildcard character is necessary for Java to properly search.

lentaing commented 4 years ago

Hi Andrew,

Thanks for your reply. I've tried the path with the wildcard--but it did not work. My work around, posted above, seemed to have resolved the issue.

I'm not sure why CLASSPATH is not being properly set in java.sh--my best guess is that it could be related to the conda environment I created for the xenoCP dependencies or perhaps is related to how cromwell interacts with conda...I'm not sure.

Regards, Len