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Dockerfile
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FROM continuumio/miniconda3:4.9.2
RUN conda config --add channels bioconda && \
conda config --add channels conda-forge && \
conda install -y -c bioconda \
python=3.7 \
fastqc=0.11.9 \
samtools=1.12 \
macs2=2.2.6 \
minimap2=2.18 \
deeptools=3.5.1 \
snakemake-minimal=5.26.0 \
multiqc=1.10.1 \
bedtools=2.30.0 \
ucsc-bedclip=377 \
ucsc-bedgraphtobigwig=377 \
trim-galore=0.6.6
# samtools fix
RUN cd /opt/conda/lib && ln -s libcrypto.so.1.1 libcrypto.so.1.0.0
# fresh sratoolkit
WORKDIR /tools
RUN wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.8/sratoolkit.2.10.8-ubuntu64.tar.gz && \
tar -vxzf sratoolkit.tar.gz
ENV PATH "$PATH:/tools/sratoolkit.2.10.8-ubuntu64/bin"
WORKDIR /project