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EBI Groups Thornton Software PoreWalkerLone Installation Instructions

PoreWalkerLone Installation Instructions

PoreWalkerLone

1. Download PoreWalkerLone

You can obtain the latest version of the PoreWalkerLone programs here:
 
PoreWalkerLone programs
 
Click on the icon on the left to download the porewalker.zip file which contains the PoreWalkerLone executables and associated files.

 
Note that the programs will only run under linux and require the following applications to be separately installed:
  • PyMOL molecular graphics program
  • ImageMagick convert
  • R package

 

2. Install the programs

Move porewalker.zip to an appropriate location and then unpack as follows:
unzip porewalker.zip
This will create a directory called porewalker, and various subdirectories beneath, containing all the necessary files.
 
 

3. Download required external packages

PoreWalkerLone requires a number of 3rd-party packages to run. These are listed below and must be installed or the programs will not be able to run properly. If your system does not already have them, a Google search will help you to find where to obtain them from.
  1. PyMOL - There are a number of versions of this program available. Many are free - or are available for free as educational versions. Any version from v.0.99 upwards is fine.

  2. ImageMagick convert - PoreWalkerLone contains many images, and the bulk of the image conversion is performed by the convert utility in the ImageMagick package, which is available from:
    https://imagemagick.org/script/download.php

  3. R package - This is used for generating various plots. It can be obtained from:
    https://www.r-project.org/

4. Editing the parameter file

Before you can run PoreWalkerLone, you need to tell the program where certain things are located so that it can find them. This is done by editing a simple text file called PARAMS, located in the directory:
porewalker/params
Only five parameters need to be edited, as shown in green below: 

###########################################################
#
# Parameters for PoreWalker scripts
#
##########################################################

#
# PoreWalker results directory
#
POREWALKER_DIR = /nfs/userapps/porewalker
RESULTS_DIR    = /nfs/data/porewalker

#
#-- Paths to required external software
#
CONVERT_EXE    = /usr/bin/convert
PYMOL_EXE      = /nfs/research1/software/Linux_x86_64/bin/pymol
R_EXE          = /usr/bin/R
The parameters you need to define are:
  • POREWALKER_DIR - This defines the directory where the PoreWalkerLone programs are installed. The correct directory will contain the following subdirectories: data, exe, params, etc.
     
  • RESULTS_DIR - This tells PoreWalkerLone the name of the directory where it is to write all its output files. This directory must exist, so make sure you create it before running the program.
     
  • CONVERT_EXE - The full path to the ImageMagick convert image conversion program.
     
  • PYMOL_EXE - The path to the PyMOL executable.
     
  • R_EXE - The path of the R package.

5. Running the program

Once you have installed all the required programs, and edited the PARAMS file as described above, you are ready to start running PoreWalkerLone.
 
Instructions can be found in:
PoreWalkerLone Manual