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1. Installation

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Breon Schmidt edited this page Jul 28, 2021 · 14 revisions

Note: These are still being tested, please let me know whether you have any issues.

Installing ALLSorts

Clone the ALLSorts git repository

Via the command line/terminal, navigate to the folder where you would like ALLSorts installed and execute:

git clone git@github.com:Oshlack/ALLSorts.git or git clone https://github.com/Oshlack/ALLSorts.git

Depending on whether you have setup SSH keys.

Dependencies

The ALLSorts installation process heavily relies on https://www.anaconda.com/. This simplifies the process of ensuring that the correct versions of dependent packages are installed. If these versions deviate, there is a risk that the output will differ than what was intended.

  1. Download and Install Anaconda

    Installation instructions for Anaconda can be found here.

  2. Create a new environment using the supplied yaml file

    Navigate to where you installed the ALLSorts package and then execute conda env create -f env/allsorts.yml.
    This will create the "allsorts" environment which you will need to activate each time you wish to use ALLSorts.

  3. Activate environment

    Depending on your Anaconda version, either of these should do the trick.
    source activate allsorts or conda activate allsorts.

  4. Install ALLSorts

    From the clone root execute: pip install .

  5. (Optional) Add ALLSorts to your path or as a reusable system variable.

    This will allow you to quickly call ALLSorts without having to navigate to the installation directory.

Run a test!

If all worked, you should be able to run a test without any issues! Just follow these steps:

  1. Create a folder where you would like the results to go, i.e. mkdir ../test_results from the ALLSorts root.
  2. python ALLSorts -samples tests/counts/test_counts.csv -destination ../test_results
  3. You will notice the results have appeared in ../test_results. For a detailed explanation of each file, visit Interpreting results.

Uninstalling ALLSorts

Sorry to see you go! Uninstalling should be really easy with Anaconda after you have deactivated (conda deactivate allsorts). conda remove --name allsorts --all

Then you just need to remove your cloned repositories for MoRP and ALLSorts.

Follow the relevant documentation on the https://www.anaconda.com/ website to uninstall conda, if required.

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