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Dockerfile
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#################################################################
# Dockerfile
#
# Software: maxATAC
# Software Version: v0.0.3
# Description: python based suite for transcription factor binding prediction
# Website: https://github.com/MiraldiLab/maxATAC
# Website2: https://github.com/MiraldiLab/maxATAC_data
# Provides: Transcription Factor Binding Prediction
# Base Image: biowardrobe2/samtools:v1.4/bedtools/ucsc-bedgraphtobigwig/pigz
# Build Cmd: docker build --rm -t miraldi/maxatac:v0.0.3 -f Dockerfile .
# Pull Cmd: docker pull miraldi/maxatac:v0.0.3
# Run Cmd: docker run --rm -ti miraldi/maxatac:v0.0.3
#################################################################
# Dockerfile, Image, Container
FROM python:3.9
################## BEGIN INSTALLATION ######################
WORKDIR /tmp
ENV VERSION_BEDTOOLS 2.26.0
ENV URL_BEDTOOLS "https://github.com/arq5x/bedtools2/releases/download/v${VERSION_BEDTOOLS}/bedtools-${VERSION_BEDTOOLS}.tar.gz"
ENV VERSION_HTSLIB 1.12
ENV URL_HTSLIB "https://github.com/samtools/htslib/releases/download/${VERSION_HTSLIB}/htslib-${VERSION_HTSLIB}.tar.bz2"
ENV VERSION_SAMTOOLS 1.12
ENV URL_SAMTOOLS "https://github.com/samtools/samtools/releases/download/${VERSION_SAMTOOLS}/samtools-${VERSION_SAMTOOLS}.tar.bz2"
ENV URL_UCSC "http://hgdownload.soe.ucsc.edu/admin/exe/userApps.src.tgz"
RUN apt-get update && \
apt-get install -y gcc-10-base libgcc-10-dev libxml2-dev libcurl4-openssl-dev libssl-dev pandoc libgtextutils-dev libmariadb-dev-compat libmariadb-dev libpng-dev uuid-dev libncurses5-dev libbz2-dev liblzma-dev pigz rsync && \
### Install htslib
wget -q -O - $URL_HTSLIB | tar -jxv && \
cd htslib-${VERSION_HTSLIB} && \
./configure --prefix=/usr/local/ && \
make -j 4 && \
make install && \
cd .. && \
### Install samtools
wget -q -O - $URL_SAMTOOLS | tar -jxv && \
cd samtools-${VERSION_SAMTOOLS} && \
./configure --prefix=/usr/local/ && \
make -j 4 && \
make install && \
cd .. && \
### Install bedtools
wget -q -O - $URL_BEDTOOLS | tar -zxv && \
cd bedtools2 && \
make -j 4 && \
cd .. && \
cp ./bedtools2/bin/bedtools /usr/local/bin/ && \
### Install UCSC User Apps
wget -q -O - $URL_UCSC | tar -zxv --strip-components=2 && \
make -j 2 && \
cp ./bin/* /usr/local/bin/ &&\
rm -rf ./* &&\
pip install maxatac==0.0.3 &&\
mkdir -p /opt/maxatac && cd /opt/maxatac &&\
git clone https://github.com/MiraldiLab/maxATAC_data.git && mv maxATAC_data data &&\
cd ./data/hg38 && wget https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.2bit &&\
strip /usr/local/bin/*; true
CMD ["maxatac"]