doku:smrtanalysis [VSC Wiki]

This version (2022/06/20 09:01) was approved by msiegel.

This is an old revision of the document!

installation

add SMRTAnalysis_HOME to your .bashrc:

echo "export SMRTAnalysis_HOME=/home/lv60000/markus/downloads/SMRT-Analysis" >> ~/.bashrc
source ~/.bashrc

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

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'

edit '[client]' section of ./smrtanalysis/userdata/database/mysql/config/etc/mysql/my.cnf:
```
[client]
user = root
password = yourpassword
```

running

allocate a node:
```
salloc -p mem_0128 --qos=normal_0128
```

start server on allocated:

srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd start

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
navigate to http://localhost:8090/ in your local browser

when finished stop the server on the compute node:

srun $SMRTAnalysis_HOME/smrtanalysis/admin/bin/smrtportald-initd stop

follow the instructions on http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Analysis-Software-Installation-v2.3.0.pdf