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Source code for LOCALIZER

The source code for running LOCALIZER locally can be found here: LOCALIZER GitHub

LOCALIZER is licensed under a GPLv3 licence with CSIRO Disclaimer

Installation

LOCALIZER has been written in Python and uses pepstats from the EMBOSS software and the WEKA 3.6 software. It also requires that you have Perl installed.

To get LOCALIZER to work on your local machine, you need to install the EMBOSS and WEKA softwares from source. Both are already provided in the LOCALIZER distribution to ensure that compatible versions are used.

1. Make sure LOCALIZER has the permission to execute. Then unpack LOCALIZER in your desired location

  • tar xvf LOCALIZER_1.0.4.tar.gz
    chmod -R 755 LOCALIZER_1.0.4/
    cd LOCALIZER_1.0.4

    • 2. For the EMBOSS installation, you need to switch to the Scripts directory and unpack, configure and make

  • cd Scripts
    tar xvf emboss-latest.tar.gz
    cd EMBOSS-6.5.7/
    ./configure
    make
    cd ../

    • 3. For WEKA, you need to simply unzip the file weka-3-6-12.zip

  • unzip weka-3-6-12.zip

    • If you are having troube installing EMBOSS, please see here for help.
    If you are having troube installing WEKA, please see here for help.

    4. Test if LOCALIZER is working

  • python LOCALIZER.py -e -i Effector_Testing.fasta

    • 5. Problems?

    Note also that you need PERL to be installed on your computer for running NLStradamus.

    Make sure that your input sequences in FASTA format have proper identifiers, if you only supply the empty identifier '>' LOCALIZER will fail.

    Contact

    For comments and suggestions regarding the code please contact jana.sperschneider@csiro.au