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--- doku:smrtanalysis [2017/01/31 11:23] – markus
+++ doku:smrtanalysis [2017/01/31 11:40] – markus
@@ Line 1: / Line 1: @@
 ==== SMRTAnalysis ====
 === installation ===
-  - Set SMRTAnalysis_HOME:<code>export SMRTAnalysis_HOME=/home/lv60000/markus/downloads/SMRT-Analysis</code>
+  - 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
@@ Line 12: / Line 14: @@
 </code>
   - Reset MYSQL password: <code>
+cd $SMRTAnalysis_HOME
 ./smrtanalysis/admin/bin/smrtportald-initd start
-export LD_LIBRARY_PATH=$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>
@@ Line 30: / Line 33: @@
   - allocate a node: <code>salloc -p mem_0128 --qos=normal_0128</code>
-  - after allocation the environment variable 'SLURM_NODELIST' contains the node to run SMRTAnalysis on:
+  - 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>