NIH | National Cancer Institute | NCI Wiki  

Error rendering macro 'rw-search'

null

Versions Compared

Old Version 45

changes.mady.by.user Unknown User (hadfielj)

Saved on

compared with

New Version 46

changes.mady.by.user Unknown User (hadfielj)

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

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).

  1. mkdir /usr/local/bioconductor/logs
  2. Edit /usr/local/activemq/conf/log4j.properties
    1. Change "log4j.rootLogger=INFO, stdout" to "log4j.rootLogger=INFO, out"
    2. Change "log4j.appender.out.file=${activemq.home}/data/activemq.log" to "log4j.appender.out.file=/usr/local/bioconductor/logs/activemq.log"
  3. cd /usr/local/bioconductor/logs
  4. ln -s /usr/local/bioconductor/caDNAcopy/nohup.out ./rworker.log
  5. ln -s $CATALINA_HOME/logs/catalina.out ./tomcat.log