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update the installation guide
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XiaoTaoWang committed Feb 17, 2023
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Expand Up @@ -26,16 +26,16 @@ enhancer-hijacking events from chromatin interaction data in re-arranged genomes

Installation
============
NeoLoopFinder and all the dependencies can be installed using either `conda <https://conda.io/miniconda.html>`_
NeoLoopFinder and all the dependencies can be installed using either `mamba <https://mamba.readthedocs.io/en/latest/installation.html>`_
or `pip <https://pypi.org/project/pip/>`_::

$ conda config --add channels r
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda config --set channel_priority strict
$ conda create -n neoloop cooler matplotlib pyensembl pybigwig intervaltree scikit-learn=1.1.2 joblib=1.1.0 rpy2 r-mgcv
$ conda activate neoloop
$ mamba create -n neoloop cooler matplotlib pyensembl pybigwig intervaltree scikit-learn=1.1.2 joblib=1.1.0 rpy2 r-mgcv
$ mamba activate neoloop
$ pip install -U neoloop TADLib pomegranate

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