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Source code for ApoplastP

The source code for running ApoplastP locally can be found here: ApoplastP_1.0.1.tar.gz

Have a look at the ApoplastP GitHub page for version history and for obtaining previous versions: ApoplastP GitHub

ApoplastP is licensed under a GPLv3 licence with CSIRO Disclaimer

Installation

ApoplastP has been written in Python and uses pepstats from the EMBOSS software and the WEKA 3.8.1 software. To get ApoplastP to work on your local machine, you need to install the EMBOSS and WEKA softwares from source. Both are already provided in the ApoplastP distribution to ensure that compatible versions are used.

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

  • tar xvf ApoplastP_1.0.1.tar.gz
    chmod -R 755 ApoplastP_1.0.1/
    cd ApoplastP_1.0.1

    • 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-3-8-1.zip

  • unzip weka-3-8-1.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 ApoplastP is working

  • python ApoplastP.py -i Testing.fasta

    • 5. Problems?

    If you are getting an error message like 'ImportError: No module named Bio', you need to install BioPython on your computer. See here for help. For example, you can try and run 'pip install biopython'.

    Contact

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