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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
.
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.If you don't want to read up on MoRP, you can follow these steps from the ALLSorts clone root
mkdir tools
cd tools
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which pip
(should be */allsorts/bin/pip) -
git clone https://github.com/breons/MoRP.git
orgit clone git@github.com:breons/MoRP.git
. cd MoRP
pip install .
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cd ../../
to return to ALLSorts root.
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Install ALLSorts
From the clone root execute:
pip install -e .
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(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.
If all worked, you should be able to run a test without any issues! Just follow these steps:
- Create a folder where you would like the results to go, i.e.
mkdir ../test_results
from the ALLSorts root. python ALLSorts -samples tests/test_counts.csv -destination ../test_results
- You will notice the results have appeared in
../test_results
. For a detailed explanation of each file, visit Interpreting results.
Sorry to see you go! Uninstalling should be really easy with Anaconda after you have deactivated (conda deactivate allsorts
).
conda remove --name allsorts --all
Follow the relevant documentation on the https://www.anaconda.com/ website to uninstall conda, if required.