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doku:smrtanalysis

SMRTAnalysis

installation

  1. add SMRTAnalysis_HOME to your .bashrc:
    echo "export SMRTAnalysis_HOME=/home/lv60000/markus/downloads/SMRT-Analysis" >> ~/.bashrc
    source ~/.bashrc
  2. Run the installer, use default optionx except for the points below:
    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
  3. Reset MYSQL password:
    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'
    
  4. edit '[client]' section of ./smrtanalysis/userdata/database/mysql/config/etc/mysql/my.cnf:
    [client]
    user = root
    password = yourpassword
    

running

  1. allocate a node:
    salloc -p mem_0128 --qos=normal_0128
  2. start server on allocated:
    srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd start
  3. create SSH tunnel
    • on the login node:
      echo "ssh -L8090:$SLURM_JOB_NODELIST:8090 `whoami`@vsc3.vsc.ac.at"
    • on your local machine: paste the command from the previous step and create the SSH tunnel
  4. navigate to http://localhost:8090/ in your local browser
  5. when finished stop the server on the compute node:
    srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd stop
doku/smrtanalysis.txt · Last modified: 2017/01/31 12:14 by markus