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Installing NGB from binaries

NGB is provided as java web-archive (war file) that could be deployed to a TOMCAT infrastructure

Environment requirements

Note: To install the software you must have administrator privileges on the system.

Verify that your system meets or exceeds the following hardware/software requirements

  • Server hardware requirements
    • CPU: 2 cores
    • RAM: 4Gb
    • HDD: 20 Gb free space
  • Server software requirements
  • Client web-browser requirements
    • Chrome (>= 56)
    • Firefox (>= 51)
    • Safari (>= 9)
    • EDGE (>= 25)

We'll refer to Tomcat installation directory as $CATALINA_HOME, assuming that NGB binary distribution is located at /home/user/catgenome.war and NGB data folder is /opt/catgenome/.

Stop Tomcat, if it is running

sudo $CATALINA_HOME/bin/catalina.sh stop

Delete $CATALINA_HOME/webapps/catgenome folder and $CATALINA_HOME/webapps/catgenome.war, if you've previously installed NGB

#Delete catgenome folder
if [ -d $CATALINA_HOME/webapps/catgenome ]
    then
       rm -Rf $CATALINA_HOME/webapps/catgenome
fi  
if [ -f  $CATALINA_HOME/webapps/catgenome.war ]
   then
      rm -f  $CATALINA_HOME/webapps/catgenome.war
fi

Copy catgenome.war to $CATALINA_HOME/webapps/ folder

cp /home/user/catgenome.war $CATALINA_HOME/webapps/

Set path to NGB configuration file for Tomcat configuration file $CATALINA_HOME/conf/catalina.properties

mkdir $CATALINA_HOME/conf/catgenome/
echo "CATGENOME_CONF_DIR=${CATALINA_HOME}/conf/catgenome/" >> $CATALINA_HOME/conf/catalina.properties

Create catgenome.properies file with NGB configuration in $CATGENOME_CONF_DIR. This file must include the following properties:

  • files.base.directory.path=/opt/catgenome/contents path for storing NGB files (Fasta, BAM, VCF, etc.)
  • database.driver.class=org.h2.Driver driver for NGB database, default database is H2
  • database.jdbc.url=jdbc:h2:file:/opt/catgenome/H2/catgenome path to NGB database location
  • database.username=catgenome user for NGB database
  • database.password= password for NGB database, may be empty
  • database.max.pool.size=25 NGB database connection pool configuration
  • database.initial.pool.size=5 NGB database connection pool configuration
echo "files.base.directory.path=/opt/catgenome/contents" > $CATGENOME_CONF_DIR/catgenome.properties
echo "database.driver.class=org.h2.Driver" >> $CATGENOME_CONF_DIR/catgenome.properties
echo "database.jdbc.url=jdbc:h2:file:/opt/catgenome/H2/catgenome" >> $CATGENOME_CONF_DIR/catgenome.properties
echo "database.username=catgenome" >>$CATGENOME_CONF_DIR/catgenome.properties
echo "database.password=" >> $CATGENOME_CONF_DIR/catgenome.properties
echo "database.initial.pool.size=5" >> $CATGENOME_CONF_DIR/catgenome.properties
echo "database.max.pool.size=25" >> $CATGENOME_CONF_DIR/catgenome.properties

If you want to enable browsing NGS files directly from server's file system, add the following properties:

  • file.browsing.allowed=true - enables file browsing from file system
  • ngs.data.root.path=/opt/catgenome - sets root of allowed to browsing file system part to /opt/catgenome. If this property is not set, root will be set to the root of file system.
echo "file.browsing.allowed=true" >> $CATGENOME_CONF_DIR/catgenome.properties
echo "ngs.data.root.path=/opt/catgenome" >> $CATGENOME_CONF_DIR/catgenome.properties

If you want to specify max number of VcfIndexEntries keeping in memory during vcf loading, add the following property. For files, which produce more entries then the number, extra entries will be spilled to disk (temp directory).

  • files.vcf.max.entries.in.memory=1000000 - 1000000 entries take about 3Gb in the heap
echo "files.vcf.max.entries.in.memory=1000000" >> $CATGENOME_CONF_DIR/catgenome.properties

If you want to disable cache for headers and indexes of VCF, GTF, BED files, change the following property. By default it is true:

  • server.index.cache.enabled=false - disables caching for headers and indexes
echo "server.index.cache.enabled=false" >> $CATGENOME_CONF_DIR/catgenome.properties

Set Tomcat configuration in the file $CATALINA_HOME/conf/server.xml by adding the following values to the "Connector" XML node

sed -i '/Connector port="8080"/,/redirectPort="8443" \ /c\<Connector port="8080" protocol="HTTP/1.1" connectionTimeout="20000" \ compression="on" compressionMinSize="2048" compressableMimeType="text/html,text/xml,application/json,application/javascript" \ redirectPort="8443"/>' $CATALINA_HOME/conf/server.xml

Start Tomcat

sudo $CATALINA_HOME/bin/catalina.sh start

NGB will be available on port 8080 (if it was not changed): http://localhost:8080/catgenome/