PrimerDesign

Support programs for primer design and picking

Prerequisites

• Debian or Ubuntu compatible operating system
• Perl and Python execution environment
• Internet connection and wget
• Compilers, headers and libraries

Assumption of directory structure

• home directory (~)
  • bin (command installation path if installPROGRAMS.sh is used)
  • blastdb (BLAST database installation path)
  • taxonomy (NCBI Taxonomy dump installation path)
  • work (working directory containing support scripts)

How to install

Download this package

wget https://github.com/astanabe/PrimerDesign/archive/master.tar.gz -O PrimerDesign-master.tar.gz
tar -xzf PrimerDesign-master.tar.gz
cd PrimerDesign-master

Install dependent packages

sh installDEPS.sh

This requires sudo password to execute.

Install required programs

sh installPROGRAMS.sh

This will install ecoPCR, Claident, Phylogears2, VSEARCH, EMBOSS, BLAST+ and R.

Install required data

sh installDB.sh

This will install NCBI nt and NCBI Taxonomy dump files.

Enabling installed commands

Above installer installs commands into ~/bin. Therefore, you need to add this path to PATH environment variable like below.

export PATH=~/bin:$PATH