INSTALL.md

maxATAC: a suite of user-friendly, deep neural network models for transcription factor binding prediction from ATAC-seq

Install Instructions

1. To install maxATAC begin by downloading the data reopository located on github: maxATAC_data

git clone https://github.com/MiraldiLab/maxATAC_data.git

2. To ensure that the data is located in a central location copy maxATAC_data to local location:

mkdir -p /opt/maxatac/data/
cp -r ./maxATAC_data /opt/maxatac/

3. Then Download hg38.2bit file from UCSC in a location of your choice

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

4. Installing maxATAC

Installing with Conda

1. Create a conda environment for maxATAC with conda create -n maxatac python=3.9 samtools wget bedtools ucsc-bedgraphtobigwig pigz

If you get an error installing ucsc-bedgraphtobigwig try conda install -c bioconda ucsc-bedgraphtobigwig

2. Install maxATAC with pip install maxatac

3. Test installation with maxatac -h

4. Download reference data with maxatac data

Installing with python virtualenv

1. Create a virtual environment for maxATAC with virtualenv -p python3.9 maxatac.

2. Install required packages and make sure they are on your PATH: samtools, bedtools, bedGraphToBigWig, wget, git, pigz.

3. Install maxatac with pip install maxatac

4. Test installation with maxatac -h

Running maxATAC with a docker

A docker image of maxATAC can be found on our lab dockerpage

1. install and run docker
2. Run docker pull miraldi/maxatac:v0.0.3 to pull the docker image onto your device
3. Run maxATAC through docker docker run --rm -ti miraldi/maxatac:v0.0.3 /bin/bash