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doku:smrtanalysis [2017/01/31 10:06] – markusdoku:smrtanalysis [2017/01/31 12:14] (current) – markus
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 ==== SMRTAnalysis ==== ==== SMRTAnalysis ====
 === installation === === installation ===
- +  - add SMRTAnalysis_HOME to your .bashrc:<code>echo "export SMRTAnalysis_HOME=/home/lv60000/markus/downloads/SMRT-Analysis" >> ~/.bashrc 
-Run the installer, use default optionx except for the points below: +source ~/.bashrc</code> 
-<code> +  - Run the installer, use default optionx except for the points below:<code> 
-start_dir=`pwd`+cd $SMRTAnalysis_HOME
 ./smrtanalysis_2.3.0.140936.run ./smrtanalysis_2.3.0.140936.run
  
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 #cores used: 16 #cores used: 16
 </code> </code>
- +  - Reset MYSQL password: <code> 
-Reset MYSQL password: +cd $SMRTAnalysis_HOME
-<code>+
 ./smrtanalysis/admin/bin/smrtportald-initd start ./smrtanalysis/admin/bin/smrtportald-initd start
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${start_dir}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql-5.1.73/lib/mysql/ +export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${SMRTAnalysis_HOME}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql-5.1.73/lib/mysql/ 
-${start_dir}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql/bin/mysqladmin -u root -S /tmp/mysql_53306.sock password 'asdf'+${SMRTAnalysis_HOME}/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/mysql/bin/mysqladmin -u root -S /tmp/mysql_53306.sock password 'asdf' 
 </code> </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]]
 +
 +
  
-=== usage === 
  • doku/smrtanalysis.1485857208.txt.gz
  • Last modified: 2017/01/31 10:06
  • by markus