The JCVI Primer Designer is largely a set of PERL scripts which depend on several commonly used externally developed bioinformatics tools. These tools have been included in the JCVI Primer Designer package to simplify installation and to prevent version incompatibility problems from arising.
Since operating system settings will change over time and differ between distributions and across platforms, installing the JCVI Primer Designer will require some patience and UNIX knowhow if your setup is somewhat different than ours.
The externally developed software that has been included with the JCVI Primer Designer include blast, dust, EMBOSS, and primer3. In addition, several PERL modules that may not be standard on all OS setups may also be tapped. In our distribution, we have attempted to include PERL modules that were not standard at our site, but if you run into any problems with “missing” PERL modules, please go to the CPAN website (http://www.cpan.org/) and try to download and install the necessary/missing PERL modules. Please feel free to contact us with problems so we may propagate our FAQ page and also include improvements in future releases. You may find that most installation problems can be resolved by looking into your environmental variables: PATH, PERL5LIB, and/or EMBOSS_ACDROOT.
To begin the installation of the JCVI Primer Designer, move the archive you have downloaded into a directory you have write permission to, and then explode the archive with the following command:
tar –xvf primer_designer_<release_date>.tgz
The <release_date> should contain the date that we created/uploaded the package, for example 20101201. When you execute the command the primer_design directory will be created and all the necessary files will be unpacked into it.
Go to (cd) into the created primer_design directory. For beginner users, this will be the directory where most of the primer design tools will be found. For more advanced user, the primer_design/PrimerDesigner directory contains the core JCVI Primer Designer software which the scripts found in primer_design depend on.
Next run the external software setup script.
This script will determine whether you are using 32-bit or 64-bit Linux, or MacOS, and try to install the correct binaries within the primer design directories. Next, the script will update configuration files so that primer design can find the binaries and PERL modules relative to where you installed the package. Once you have done this, you should try running through one of the examples provided to confirm that the setup was successful prior to trying your own dataset.