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1. Installation

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Breon Schmidt edited this page Jun 30, 2020 · 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 Median of Ratios Python (MoRP)

    This is a little normalisation package I made that ALLSorts relies upon. To install, simply follow the instructions here.

    Note: Make sure you have the conda environment enabled and are using the pip within this environment. You can check with which pip. It's no big deal if you don't, but it just means that you can remove MoRP along with ALLSorts if you want to.

    If you don't want to read up on MoRP, you can follow these steps from the ALLSorts clone root

    1. mkdir tools
    2. cd tools
    3. which pip (should be */allsorts/bin/pip)
    4. git clone https://github.com/breons/MoRP.git or git clone git@github.com:breons/MoRP.git.
    5. cd MoRP
    6. pip install .
    7. cd ../../ to return to ALLSorts root.
  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.

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