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Dockerfile
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FROM ubuntu:20.04
################## METADATA ######################
LABEL about.summary="Collection of tools for the BSF atacseq_pipeline"
LABEL about.home="https://www.biomedical-sequencing.org"
LABEL about.tags="Epigenetics, ATAC-seq"
LABEL about.maintainer="Bekir Erguener @ CeMM/BSF"
LABEL version="0.2"
################## MAINTAINER ####################
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y --no-install-recommends \
g++ \
gcc \
make \
autoconf \
wget \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
parallel \
pigz \
alien \
zip \
unzip \
python3.8 \
python3.8-dev \
python3-pip \
bedtools \
bowtie2 \
&& apt-get -y clean && apt-get -y autoclean && apt-get -y autoremove
RUN pip3 install deeptools==3.5.0 \
macs2==2.2.7.1
# Compile BWA
WORKDIR /root/source
RUN wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 \
&& tar -xf bwa-0.7.17.tar.bz2
WORKDIR /root/source/bwa-0.7.17
RUN make
# Compile bcftools
WORKDIR /root/source
RUN wget https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2 \
&& tar -xf bcftools-1.11.tar.bz2
WORKDIR /root/source/bcftools-1.11
RUN ./configure \
&& make
# Compile samtools
WORKDIR /root/source
RUN wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 \
&& tar -xf samtools-1.11.tar.bz2
WORKDIR /root/source/samtools-1.11
RUN ./configure --without-curses \
&& make
# Compile samblaster
WORKDIR /root/source
RUN wget https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.24/samblaster-v.0.1.24.tar.gz \
&& tar -xf samblaster-v.0.1.24.tar.gz
WORKDIR /root/source/samblaster-v.0.1.24
RUN make
# Compile fastp
WORKDIR /root/source
RUN wget https://github.com/OpenGene/fastp/archive/v0.20.1.tar.gz \
&& tar -xf v0.20.1.tar.gz
WORKDIR /root/source/fastp-0.20.1
RUN make
RUN cp /root/source/bwa-0.7.17/bwa \
/root/source/bcftools-1.11/bcftools \
/root/source/samtools-1.11/samtools \
/root/source/samblaster-v.0.1.24/samblaster \
/root/source/fastp-0.20.1/fastp /usr/local/bin/
WORKDIR /homer
RUN wget http://homer.ucsd.edu/homer/configureHomer.pl \
&& perl configureHomer.pl -install \
&& perl configureHomer.pl -install hg38 mm10
ENV PATH /homer/bin:$PATH
RUN apt-get update && apt-get install -y --no-install-recommends \
git
RUN pip3 install multiqc
RUN git clone https://github.com/berguner/atacseq_pipeline.git && \
python3 atacseq_pipeline/multiqc_atacseq/setup.py install
CMD ["/bin/bash"]