UTGB Toolkit Index

FAQ

How do I set maximum memory size when running UTGB server?

Use JVM_OPT variable to set JVM options: 

$ JVM_OPT="-Xmx1g" utgb server -g

How do I tell the UTGB Toolkit to use my proxy server?

Edit $(HOME)/.m2/settings.xml file and add proxies element as follows: 

<settings>
  ...
  <proxies>
    <proxy>
      <id>myproxy</id>
      <active>true</active>
      <protocol>http</protocol>
      <host>proxy.somewhere.com</host>
      <port>8080</port>
      <username>proxyuser</username>
      <password>somepassword</password>
    </proxy>
  </proxies>
  ...
</settings>

Somthing went wrong. What should I do?

Update several libraries with the following command: 

> utgb maven compile -U

Or remove temporary folders: 

> rm -rf target

When some files are gone, how do I recover them?

The utgb shell provides repair command for reproducing missing files and reverting the modified files: 

> utgb repair
myapp> utgb repair
[ScaffoldGenerator]     output folder: ./
[ScaffoldGenerator]     package  = myapp4
[ScaffoldGenerator]     explodedWebappDir        = target/utgb
[ScaffoldGenerator]     projectName      = myapp4
[ScaffoldGenerator]     moduleName       = myapp4.gwt.UTGBEntry
[ScaffoldGenerator]     group    = org.utgenome.track
[ScaffoldGenerator]     create a directory: ./tomcat
[ScaffoldGenerator]     create a directory: ./tomcat/webapps
[ScaffoldGenerator]     create a directory: ./tomcat/webapps/ROOT
[ScaffoldGenerator]     create a directory: ./tomcat/webapps/ROOT/WEB-INF
File ./config/track-config.xml already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: n

File ./db/README already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: 
File ./pom.xml already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: n

File ./README already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: 
File ./src/assembly/jar.xml already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: n

File ./src/main/webapp/404.jsp already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: 
File ./src/main/webapp/image/utgb.gif already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: n

File ./src/main/webapp/index.jsp already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: 
File ./src/main/webapp/view/default-view.xml already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: n

File ./src/main/webapp/WEB-INF/web.xml already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: 
[ScaffoldGenerator]     create a file: ./tomcat/webapps/ROOT/WEB-INF/web.xml
File ./www/README already exists.
Overwrite it? (y: yes, n: no, A: yes to all, X: no to all) [n]: X