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When you start CellProfiler set the CellProfiler plugins directory to the
cp_pluginsdirectory, and the ImageJ plugin directory to theij_pluginsdirectory. -
Set the
CLASSPATHenvironment variable to include the jarsDImageSVN_.jarandjsch.jarin thejarlibdirectory. There are various ways to set the classpath. For general instructions (Windows and Linux) see here.(Linux) Another way to set the classpath is on application basis like I did on the server in the
/usr/local/bin/cellprofilerscript:#!/bin/sh # # Wrapper script used to start CellProfiler on Linux. PREFIX=/opt/cellprofiler export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/amd64/server export CLASSPATH=/data/shared/cellprofiler_plugins/jarlib/DImageSVN_.jar:/data/shared/cellprofiler_plugins/jarlib/jsch.jar python2 $PREFIX/CellProfiler/CellProfiler.py "$@"
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(Linux) Make sure python-suds is available.
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