We are going to call your install directory $BIOCORE_HOME. EVERYWHERE YOU SEE $BIOCORE_HOME REPLACE IT WITH YOUR CHOSEN DIRECTORY.
To make it easy for you to update BioCoRE as we release new code, you need to create an rc file in your home directory that can be used by our install scripts.
Download the
following from here, or copy the following into the file
.biocoreInstallrc in your home directory. Note, because
of HTML, you might have extraneous <FONT> tags in your code if
you simply copy it from below. We suggest you follow the link above,
which doesn't have the extraneous font tags.
# Locations of paths to external biocore jars. If you have followed
# the instructions on the web, you should only need to change the
# very first value for the $BIOCORE_HOME
# This file is included by an sh install script that the person
# installing the server will execute before starting up the server
# binary.
# Base path where all of the biocore packages are installed. This
# variable isn't used directly. Rather, it is used as a prefix for
# variables defined below this.
if [ -z "$biocoreBase" ]; then
biocoreBase=$BIOCORE_HOME
fi
# BioCoRE webapp name (what you type after the http://machine/. Probably
# don't need to change
if [ -z "$biocoreWebAppName" ]; then
biocoreWebAppName=biocore
fi
# Location of the biocore servlet files
if [ -z "$biocoreServletContainerDir" ]; then
biocoreServletContainerDir=${biocoreBase}/packages/tomcat/current
fi
# Location of the jep jar file
if [ -z "$jepJar" ]; then
jepJar=${biocoreBase}/packages/jep/current/jep.jar
fi
# Location of the mysqlj jar file. If you didn't download a new
# connector, don't worry about this
#if [ -z "$mysqlJ" ]; then
# mysqlJ=${biocoreBase}/packages/mysqlj/current/mysqlj.jar
#fi
You need to replace the values with values for your system. If you
have used the exact directories suggested during the installation
you probably will only need to edit the first item for the
biocoreBase. However, we suggest that you look over
the other items as well.
So, the biocoreBase would end up looking something like:
biocoreBase=/usr/local/biocore
This file, the .biocoreInstallrc file, will be needed
anytime you update the BioCoRE server software. So, just leave it in
your HOME directory and it will make the upgrade process much easier
since you won't have to recreate the file.
If you downloaded and installed your own version of the MySQL Connector, uncomment that section of the file.
Once you have this file set up, you need to run the script
install.sh that came in your original tar file that you
downloaded. The file might not be set to executable. If this is the
case, you will need to chmod it first before you can execute it. Feel
free to look at it if you wish. The install script copies over needed
files into the proper Tomcat directories and will need to be run in the
future anytime that you update the BioCoRE server. It should tell you
that it is done and you can now start Tomcat.
Next Step: More BioCoRE Configuration.
Back to the installation page
Feedback
The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.
