PSORTb is a bioinformatics tool for predicting subcellular localization for a given set of protein sequences. The protein sequences must belong to one type of organisms, classified by cell membrane type in order to more accurately predict subcellular localization. The supported organism types are:
- Gram negative (-n)
- Gram positive (-p)
- archaea (-a)
- Gram negative without outer membrane
- Gram positive with outer membrane
The PSORTb program has been added to a Docker container to simply the installation process.
This PSORTb installations uses PSORTb version 3.
This repository hosts a Docker buildfile (Dockerfile) which builds the complex environment of PSORTb. It also contains a wrapper script (named psortb) to run the PSORTb analysis inside the Docker container.
Warning: Users of this app must have admin rights to run docker commands. Either that or an administrator must give you access to run "docker run" commands.
A pre-built image created by the Dockerfile in this repository can be found at https://hub.docker.com/r/brinkmanlab/psortb_commandline/
You can build the Docker image yourself using the following instructions. This build requires a unix-type system and 3.9GB space.
% git clone https://github.com/brinkmanlab/psortb_commandline_docker.git
% cd psortb_commandline_docker
% sudo docker build --rm --no-cache -t psortb_commandline_docker .
Once the Docker image has been installed, run PSORTb like this:
% cd psortb_commandline_docker
% ./psortb -h
Warning: Users of this psortb app must have admin rights to run docker commands. Either that or an administrator must give you access to run "docker run" commands.
% ./psortb -i <FASTA format sequence file> -r <local results directory>
PSORTb is distributed under GNU General Public License Version 3.
Please email any questions to psort-mail@sfu.ca
This application was developed by Gemma Hoad in the Brinkman Laboratory at Simon Fraser University, Greater Vancouver, Canada.