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One disadvantage to having multiple separate processes for Bioconductor is that each process creates a separate log file by default. By using the following steps, the log files for Tomcat, ActiveMQ, and caDNAcopy/caCGHcall are placed into a single directory, /usr/local/bioconductor/log}}s. If the scripts in #Optional Improvements are used, it further improves logging by placing all messages into a single log file, {{/usr/local/bioconductor/logs/bioconductor-combined.log.

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