PrimerTK is a primer toolkit to assist in standard primer design, multiplex primer design, and primer design around complex structural variants.
- python3
- primer3
- in silico PCR
If you install via git clone, PrimerTK comes with a helper script to install in silico PCR and primer3.
This helper script will also be available via pip install, but will be located in your python specific site-packages location.
NOTE: PrimerTK relies upon isPcr and primer3 which are external packages. Please verify that you have permissions to use those tools prior to installing them.
We use the installer.sh script to install these packages. Once you have verified that you have proper permissions based on their respective licenses modify installer.sh as needed for your site.
This will put primer3 and isPcr in your ~/bin/
Install all packages via git clone:
# Cloning the PrimerTK repository
$ git clone https://github.com/stjude/PrimerTK.git
$ cd PrimerTK/scripts
$ ./installer.sh
$ cd ..
$ pip3 install . --user # can install to root as well.Install all packages via pip:
# pip installing primer_tk and installing 3rd party programs using installer.sh
$ pip3 install primer_tk --user
$ cd ~/.local/lib/python3.x/site-packages/primer_tk/scripts
$ ./installer.shTo ensure that PrimerTK was installed correctly, type primer_tk -h:
usage: primer_tk [-h] [-v]
{iterator,iterator_sv,pre,pre_sv,post,post_sv,tabix} ...
positional arguments:
{iterator,iterator_sv,pre,pre_sv,post,post_sv,tabix}
Actions
iterator Iterator subparser
iterator_sv iterator_sv subparser
pre Preprocessing for snv/indel
pre_sv Preprocessing for SV's
post Parses info from pcr_output
post_sv Parses info from pcr_output
tabix Tabix subparser
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
PrimerTK is intended to be run as a workflow broken up in the following way:
primer_tk iterator --> primer3 --> primer_tk pre --> isPcr --> primer_tk post --> primer_tk tabix