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1. Installation
Note: These are still being tested, please let me know whether you have any issues.
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.
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.
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Download and Install Anaconda
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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
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This will create the "allsorts" environment which you will need to activate each time you wish to use ALLSorts. -
Activate environment
Depending on your Anaconda version, either of these should do the trick.
source activate allsorts
orconda activate allsorts
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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. -
(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.