brinkmanlab/psortb repository overview

⁠PSORTb

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 organism, classified by cell membrane type in order to more accurately predict subcellular localization. The supported organism types are:

• Gram negative
• Gram positive
• Archaea
• 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 installation uses PSORTb version 3.

Please note there is also a command line version of PSORTb available at https://hub.docker.com/r/brinkmanlab/psortb_commandline⁠.

⁠Installing this image

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.

This image takes up 1.66GB space.

Download and run the Docker image:
% sudo docker run -d -p [my preferred port]:80 -e NODE_ENVIRONMENT="production" --restart=always brinkmanlab/psortb:3.0.6
You can see this in an internet browser at http://localhost:88⁠ (or whichever port you specified in the docker run command).

OR simply download the Docker image
% sudo docker pull brinkmanlab/psortb:3.0.6

⁠Github repository

For administrators wanting to customize the Docker setup, the Dockerfile used to build this image can be found on GitHub: https://github.com/brinkmanlab/psortb-docker⁠. The Dockerfile builds the complex environment of PSORTb. The repository also contains a wrapper script (named psortb) to run the PSORTb analysis inside the Docker container (i.e a wrapper for the "docker run" command).

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.

⁠Versions

May 2019: Tag 3.0.6 - this is the first PSORTb web service Docker image hosted directly by the Brinkman Lab on Docker Hub. This is an updated version of the Docker image found at https://hub.docker.com/r/lairdm/psortb⁠, hosted by former lab member Matt Laird. Version 3.0.6 contains updated blast database libraries of proteins of confirmed subcellular localization.

⁠License

PSORTb is distributed under GNU General Public License Version 3.

⁠Support

Please email any questions to [email protected]⁠

This application was developed by Matt Laird and Gemma Hoad of the Brinkman Laboratory at Simon Fraser University, Greater Vancouver, Canada.