Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision		 Previous revision
Last revisionBoth sides next revision
doku:smrtanalysis [2017/01/31 10:08] – markusdoku:smrtanalysis [2017/01/31 11:40] – markus
Line 1: Line 1:
 ==== 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
  
Line 13: Line 13:
 #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>
 +
  
-=== usage === 
  
  
-./smrtanalysis/admin/bin/smrtportald-initd start 
  
  
  • doku/smrtanalysis.txt
  • Last modified: 2017/01/31 12:14
  • by markus