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Last pushed: 4 months ago
Short Description
PSORTb command line tool
Full Description

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 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 installation uses PSORTb version 3.
 

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 2.55GB space.

% sudo docker pull brinkmanlab/psortb_commandline:1.0.0

Once the Docker image has been installed, the following script can be installed to simplify the running of PSORTb analyses:

% wget https://raw.githubusercontent.com/brinkmanlab/psortb_commandline_docker/master/psortb
% chmod +x psortb

Warning: Users of this psortb app must have admin rights to run docker commands. Either that or an administator must give you access to run "docker run" commands.
 

Running a PSORTb analysis

Once the Docker image has been installed, run an PSORTb analysis like this:

% ./psortb -h
% ./psortb -i <FASTA format sequence file> -r <local results directory> [--positive|--negative|--archaea]

 

Github repository

For administrators wanting to tweak the Docker setup, the Dockerfile used to build this image can be found on GitHub:
https://github.com/brinkmanlab/psortb_commandline_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.
 

License

PSORTb is distributed under GNU General Public License Version 3.
 

Support

Please email any questions to psort-mail@sfu.ca

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

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Owner
brinkmanlab

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