JCVI Primer Designer Files

The following is a quickstart guide on how to install the necessary tar files.

Documentation on how to run the primer design pipeline can be found in the primer_design.tar.gz file.

DISKSPACE REQUIREMENTS:  
The human reference genome (homo_sapiens.tar.gz) is 3.7GB.  If designing many primers on this genome, at lead 5 GB of diskspace should be allocated to primer design.

OS REQUIREMENTS: 
The primer design software can be run on any Unix based OS.  However, the dependent 3rd party binaries that are used during primer design and are included in this package are compiled for 32-bit SUSE.  The primer design software can easily be configured to use locally installed versions of these binaries.  Please see the documentation in the primer_design.tar.gz file.


1. Download the primer_design.tar.gz file into a unix space.

2. From within the directory where you have put the tar file, type
	tar -xvzf primer_design.tar.gz

   This will create a primer_design directory containing all the necessary code to run the pipeline.


3. Type
	cd primer_design/reference

   to go the reference directory


4. Download the necessary reference genome tar.gz file(s) that you will need to design primers.  These reference genomes, such as homo_sapiens.tar.gz, can be found above.  Put the file(s) into the 'reference' directory that you are currently in.

   Note: These are large files and may take a while to download

   If you are using your own reference genome that is not provided on our download site, skip to step 6.


5. For each reference tar file that you have copied into this reference directory type
	tar -xvzf [NAME OF GENOME].tar.gz


6. Type
	cd ..

   to get back to the primer design directory.


7.  Follow the directions in the PCR_Primer_Design-README file found in this directory to run the primer design pipeline.  For your convenience, there is a text version and a Word Doc version of this file.