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~/transmart/transmart-data/vars
~/transmart/transmart-data/env/data-integration
~/transmart/transmart-data/env/tranSMART-ETLtransmart-etl or ~/transmart/transmart-etl
~/transmart/transmart-data/R/root/bin

Furthermore, Rserve should be evident in the following commands (the second and third issued after R starts, indicated by that change in prompt character from $ to >)

$R
>library(Rserve)
>q(save='no')

And SOLR should be evident. Start it with:

cd ~/transmart/transmart-data
. ./vars
make -C solr start &

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R CMD Rserve --version

And SOLR should be evident. Start it with:
sudo systemctl start solr

Then browse to the web location:
http://localhost:8983/solr/#/

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Finally, the configuration files should show up as:

/usrvar/sharelib/tomcat7tomcat8/.grails/transmartConfig/

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cd ~/transmart/transmart-data
. ./vars
$PGSQL_BIN/psql postgres
(use \q to quit)

Also you should be able to verify that the transmart web application can access the data base by checking the following SQL commands (alternate prompts indicate commands in PostgreSQL). The select of username should return one row without error. If searchapp is not found then you have not loaded the database correctly. It the command to run psql (e.g. $PGSQL_BIN/psql ) fails with ".../psql command not found" or "database 'transmart' does not exist' then, see further checks below.

cd ~/transmart/transmart-data
. ./vars
$PGSQL_BIN/psql transmart
>select username from searchapp.search_auth_user where username='guest';
(use \q to quit)

If there was some problem with the psql command or the select, check the following

cd ~/transmart/transmart-data
. ./vars
echo $PGSQL_BIN

Should return sudo -E -u postgres /usr/bin .

which psql

Should return /usr/bin/psql

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Tomcat will need to be running (tomcat7 tomcat8 is used here). The default installation on Ubuntu 18.04 will present a service that supports the following commands:

  • sudo service tomcat7 systemctl status tomcat8
  • sudo service tomcat7 systemctl start tomcat8
  • sudo service tomcat7 systemctl stop tomcat8
  • sudo service tomcat7 systemctl restart tomcat8

The status command returns text (to standard out) indicating if tomcat is running not. The start, stop, and restart commands do as they say. The restart command will stop and start tomcat; it can be used if tomcat is already stopped, in which case it will not attempt to stop tomcat cat, but will simply restart it.

Note that, as installed, Tomcat7 is not set up with enough stack memory to support tranSMART. Check that this has been fixed. On the ubuntu installation presented in the instructions, this option is inserted into the default parameter file for tomcat7 at /etc/default/tomcat7. In the case of the ubuntu install, check this setting with:

grep "JAVA_OPTS" /etc/default/tomcat7

You should see a line that looks like this, the important feature of which is the setting of -Xmx2g which indicated the maximum heap size:

JAVA_OPTS="-Djava.awt.headless=true -Xms512m -Xmx2g -XX:+UseConcMarkSweepGC"

NOTE: That this will cause a failure of Tomcat to start if the VM memory is not large enough. 

War Files

Have transmart.war and gwava.war been install? Did they expand correctly? Was transmart.log generated? And does catalina.out show that transmart was started. 

The following files, and dirs should exist:

cd /var/lib/tomcat7tomcat8/webapps/
ls transmart.war transmart gwava.war gwava
cd /var/lib/tomcat7tomcat8/logs
ls -al catalina.out transmart.log

Grep transmart.log for the phrase phrase 'initialization coompleted' and check the date/time match the latest system or server (re)start.

Web Site

Is the tranSMART web application running? Can you log in? Is the example data available?

Use a browser to check that the following URL's URLs return a page. For the transmart login pages the initial administrative login is, username=admin, password=admin.

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http://localhost:8080/transmart/datasetExplorer/index

On the datasetExplorer page you should see a "tree" display on the left with a top level entry "Public Studies". Expanding this entry (click on the '+') should reveal a study 'GSE8581' .