This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong. ==== SMRTAnalysis ==== === installation === - add SMRTAnalysis_HOME to your .bashrc:<code>echo "export SMRTAnalysis_HOME=/home/lv60000/markus/downloads/SMRT-Analysis" >> ~/.bashrc source ~/.bashrc</code> - Run the installer, use default optionx except for the points below:<code> cd $SMRTAnalysis_HOME ./smrtanalysis_2.3.0.140936.run #DNS name: localhost #TOMCAT port: 8090 (8080 in use by cmd) #TMP directory [/tmp/smrtanalysis] ??? #job management system: NONE #cores used: 16 </code> - Reset MYSQL password: <code> cd $SMRTAnalysis_HOME ./smrtanalysis/admin/bin/smrtportald-initd start export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${SMRTAnalysis_HOME}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql-5.1.73/lib/mysql/ ${SMRTAnalysis_HOME}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql/bin/mysqladmin -u root -S /tmp/mysql_53306.sock password 'asdf' </code> - edit '[client]' section of ./smrtanalysis/userdata/database/mysql/config/etc/mysql/my.cnf: <code> [client] user = root password = yourpassword </code> === running === - allocate a node: <code>salloc -p mem_0128 --qos=normal_0128</code> - start server on allocated: <code>srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd start</code> - create SSH tunnel * on the login node: <code>echo "ssh -L8090:$SLURM_JOB_NODELIST:8090 `whoami`@vsc3.vsc.ac.at"</code> * on your local machine: paste the command from the previous step and create the SSH tunnel - navigate to http://localhost:8090/ in your local browser - when finished stop the server on the compute node: <code>srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd stop</code> - follow the instructions on [[http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Analysis-Software-Installation-v2.3.0.pdf]] doku/smrtanalysis.txt Last modified: 2017/01/31 12:14by markus