how to install jCowboy

Welcome to the jCowboy server installation walkthrough… here’s how to do it:

  • download the jcowboy jar file
  • download the jar files for jruby-support,mail-support, and j2sdkee-support
  • it might be best to store all the additional jar files in a jar-lib directory which should look a little bit like this:
    	     user@host:~/jcowboy/lib-jar/$ ls -l
    	     -rw-r--r--    1 jcowboy  jcowboy    716139 Jan 16 18:56 ant.jar
    	     -rw-r--r--    1 jcowboy  jcowboy    105573 Jan 16 18:56 bsf.jar
    	     drwxr-xr-x   13 jcowboy  jcowboy      4096 Jan 16 18:59 j2sdkee1.2.1
    	     -rw-r--r--    1 jcowboy  jcowboy     65368 Jan 16 18:56 jakarta-oro-2.0.6.jar
    	     drwxrwxr-x    8 jcowboy  jcowboy      4096 Jan 16 18:56 mail.jar
    	     -rw-r--r--    1 jcowboy  jcowboy    796402 Jan 16 18:56 jruby.jar
    	     
    	     user@host:~/jcowboy/lib-jar/$
    
  • the next step is, to add all required .jar files to your java CLASSPATH. For this to work it is necessary to edit the login script file (e.g. .bashrc in $HOME):
    	     export CLASSPATH=$CLASSPATH:~/jcowboy/lib-jar/bsf.jar:~/jcowboy/lib-jar/j2sdkee1.2.1/lib/j2see.jar:~/jcowboy/lib-jar/mail.jar:~/jcowboy/jcowboy.jar
    

    Important: don’t forget to add jcowboy.jar to your CLASSPATH as well!

  • those changes to the script file will affect the environment after the next login, so we take a little shortcut and update the environment on the fly:
    	    user@host:~/jcowboy/lib-jar/$ export CLASSPATH=$CLASSPATH:~/jcowboy/lib-jar/bsf.jar:~
    	    /jcowboy/lib-jar/j2sdkee1.2.1/lib/j2see.jar:~/jcowboy/lib-jar/mail.jar:~/jcowboy/jcowboy.jar
    	    user@host:~/jcowboy/lib-jar/$ echo $CLASSPATH
    	    .:/home/user/jcowboy/lib-jar/bsf.jar:/home/user/jcowboy/lib-jar/j2sdkee1.2.1/lib/j2see.jar:
    	    /home/user/jcowboy/lib-jar/mail.jar:/home/user/jcowboy/jcowboy.jar
    	    user@host:~/jcowboy/lib-jar/$
    
  • we’re almost done… now all we have to do is download and install the additional software that jCowboy uses for predictions:
    • Modeller http://guitar.rockefeller.edu/modeller/modeller.html
    • Prove (location currently unknown :/)
    • Anolea http://protein.bio.puc.cl/cardex/software/
    • NCBI tools (BLAST etc) http://www.ncbi.nlm.nih.gov/Ftp/
  • in the last and final step you need to edit the default.conf file, and define the binary locations for the external tools and enter information as for example mail account info, etcpp
  • Congratulations! You should now be able to use the jcowboy server :)