Decide where (on your filesystem) you are going to install the server software. You will need 50-150 megabytes (approximately) to install the various packages that are needed by BioCoRE. This number is only an estimate and depends on the operating system, etc. An install on Linux using RPMs when possible used about 100 megs of space (NOT including the space already mentioned for MySQL in the previous page) So, if space is an issue for you you might have to modify the following instructions appropriately. At any rate, for the purposes of this discussion, we are going to call this directory $BIOCORE_HOME. EVERYWHERE YOU SEE $BIOCORE_HOME REPLACE IT WITH YOUR CHOSEN DIRECTORY.
"Installation" of Java
In $BIOCORE_HOME
create a subdirectory called java. In the
java directory, uncompress the java tar file that you
downloaded. This should create a directory like
j2sdk1_4_2. In the java directory, make a
symbolic link:
ln -s j2sdk1_4_2 current
This will create a sym link called current and point it towards
the current version of java. This allows you to easily upgrade versions of
java in the future and not affect the rest of your software (like
BioCoRE) that is using it.
If you chose to use a Linux RPM, the RPM probably put java in
/usr/java/something/. Find this directory and
remember the
location, as you will need it later. Anytime in these directions
that something is
specified as being in the java directory, you need to point to the
correct directory.
"Installation" of the Java Expression Parser (JEP)
The BioCoRE server is capable of using the Java Expression Parser to allow users to calculate math expressions via their Control Panel. It is not, however, required and it is totally up to you as to whether or not you wish to provide it. (It can be a handy thing for users) The package can be downloaded from:
http://www.singularsys.com/jep
Once you have downloaded the package,
In $BIOCORE_HOME/packages/
create a subdirectory called jep. In the
jep directory, uncompress the tar file that you
downloaded. This should create a directory like
jep-2.3.0. In the jep directory, make a
symbolic link:
ln -s jep-2.3.0 current
This will create a symbolic link called current and point
it towards the current version of jep. In addition, after switching to
the current directory, create a symlink from the JAR file
to jep.jar
ln -s jep-2.3.0.jar jep.jar
"Installation" of the MySQL Connector/J
If you are using Mysql version 4.1 or higher, you need to install a newer version of MySQL Connector than BioCoRE is distributed with (due to licensing issues). Also, the version that you can download from MySQL is reported to be somewhat faster than the version that BioCoRE is distributed with.
Once you have downloaded the package,
In $BIOCORE_HOME/packages/
create a subdirectory called mysqlconnectorj. In the
mysqlconnectorj directory, uncompress the tar file that you
downloaded. This should create a directory like
mysql-connector-java-3.0.17-ga.
In the mysqlconnectorj directory, make a
symbolic link:
ln -s mysql-connector-java-3.0.17-ga current
This will create a sym link called current and point it towards
the current version of jep. In addition, after switching to the
current directory, create a symlink from the JAR file to
mysql.jar
ln -s mysql-connector-java-3.0.17-ga-bin.jar mysql.jar
Next Step: Install the Tomcat Servlet Engine.
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.
