==== 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]]