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Dockerfile
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FROM rocker/tidyverse
# Builds on Ubuntu LTS
ENV DEBIAN_FRONTEND noninteractive
WORKDIR /home
RUN mkdir /home/scripts/ /home/01_genotypes/ /home/02_LD/ /home/03_ROH/ \
/home/04_PCA/ /home/05_BLUPF90/
RUN apt-get -y update
RUN apt-get -y install plink1.9
RUN apt-get -y install python3
RUN apt-get -y install python3-pip
RUN apt-get -y install less
RUN apt-get -y install bsdmainutils
RUN pip install pandas==2.0.3
RUN apt-get -y install nano
RUN apt-get -y install glances
RUN mv /usr/bin/plink1.9 /usr/bin/plink
ADD scripts/ /home/scripts/
RUN cp /home/scripts/extract_ped.sh /home/05_BLUPF90/extract_ped.sh
RUN cp /home/scripts/prepare_snp_file.sh /home/05_BLUPF90/prepare_snp_file.sh
RUN mv /home/scripts/renumf90 /home/05_BLUPF90/renumf90
RUN mv /home/scripts/blupf90 /home/05_BLUPF90/blupf90
RUN mv /home/scripts/renum.txt /home/05_BLUPF90/renum.txt
RUN mv /home/scripts/renum_genomic.txt /home/05_BLUPF90/renum_genomic.txt
RUN /usr/local/bin/R --no-restore --file=scripts/R_packages.R > scripts/R_packages.txt
RUN chmod -R 755 scripts/
RUN chmod -R 755 05_BLUPF90/
RUN mv /home/05_BLUPF90/renumf90 /usr/bin/renumf90
RUN mv /home/05_BLUPF90/blupf90 /usr/bin/blupf90
RUN ulimit -s unlimited
RUN export OMP_STACKSIZE=64M
CMD /bin/bash