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Computer Scientist at the Department of BioSciences, Rice University

Installing and setting up KINSOLVER in a Linux 2.6.32-358.6.2.el6.x86_64

Steps that I followed to install KINSOLVER in a linux-box 2.6.32-358.6.2.el6.x86_64

  1. Get the KINSOLVER C++ source code
    1. Created folder ~/kin_c_source
    2. Downloaded Makefile, kin.cpp, kin.h
    3. Compiled executable via command-line: make
    4. Make folder ~/kin
    5. Copy executable kin_c to ~/kin/
    6. The backend simulator (executable) is then located at ~/kin/kin_c
  2. Get the Java KINSOLVER source code
    1. Created folder kin_java_source
    2. Downloaded Java files (Dataset.java, KinFile.java, …, and )
    3. Update PlotServlet.java to make sure that the URL is updated accordingly (e.g., change from genetics.uga.edu to your own server)
    4. Update the script to compile (compile.sh)
      1. The jar file for servlets may need to be specifies, such as using the one in apache tomcat. Example: /opt/apache-tomcat-7.0.40/lib/servlet-api.jar
  3. Make sure Gnuplot works
    1. For example, admin had it installed at: /usr/bin/gnuplot
  4. Setup java-servlets
    1. Inside folder ‘jsdk2.1’, update variables inside of file: kin_environment.properties
    2. Start the servlet-server by running ./startserver
      1. Verify that the servlets are running by going to http://odyssey.bioinformatics.uga.edu:8090/kin/servlet/Setup , which is a servlet that keeps track of the options needed to  run KINSOLVER
      2. In the case that the browser takes a while to show anything and times out, then likely the port (i.e., 8090) is not accessible either in the network (such as inside campus computers) or the linux-box has the port closed (system-administrator needs to open the port)
    3. Go to servlet with configuration options, save changes, and click on “create web page”
  5. Test via uploading an input file
  6. Troubleshoot until it works
    1. For example, I changed ‘kinnew’ to ‘kin’ in order to have simpler URLs
    2. Reminder: changes on java-servlets code requires stopping the server and starting it up again to be visible
      1. Inside folder ~/jsdk2.1
      2. Start server: ./startserver &
      3. Stop server: ./stopserver
        1. In case of error messages when stopping it, just ignore them.

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