Jemboss Standalone Version

This page describes how to set up a "standalone" (non client-server) Jemboss. This allows the users to run Jemboss from any machine that has the EMBOSS installation directories mounted on it. This does not really on a client-server connection but directly calls the EMBOSS applications and results are stored in the directory the user runs Jemboss from. It should be noted that the main development of Jemboss is for the client-server scenario but this installation may be suitable for small groups of users on a unix platform.

Note: java1.3 or higher should be used.

1. Download

  • Get the latest version of EMBOSS (which contains Jemboss)

    • ftp://emboss.open-bio.org/pub/EMBOSS/   (see EMBOSS download)
    gunzip EMBOSS-3.x.x.tar.gz
    tar xvf EMBOSS-3.x.x.tar
     
    2. Install Script

    This install script automates most of the Jemboss server installation and the associated EMBOSS configuration and installation.

    The script asks for the locations of the EMBOSS download, EMBOSS installation and Java directories. A jemboss.properties file is that defines the locations of the EMBOSS installation directories and environment.

    Notes for MacOSX installation.

    Go to the directory where the script should be run from:

    cd EMBOSS-3.x.x/jemboss/utils

    Run the install-jemboss-server.sh script.
    ./install-jemboss-server.sh.
     
    3. After Running the Script

    Go to the jemboss directory in the EMBOSS install directory ($EMSBOSS_INSTALL/share/EMBOSS/jemboss) and try running Jemboss. Edit runJemboss.csh to set the following environment variables:

    setenv EMBOSS_INSTALL /usr/local/emboss/
    setenv LD_LIBRARY_PATH $EMBOSS_INSTALL/lib

    For MacOSX also add:
    setenv DYLD_LIBRARY_PATH $EMBOSS_INSTALL/lib

    For HPUX also add:
    setenv SHLIB_PATH $EMBOSS_INSTALL/lib

    Also add the 'local' option for Jemboss to run in 'standalone' mode:

    java org/emboss/jemboss/Jemboss local &

    Then try running it by typing ./runJemboss.csh.