Dockerfile

FROM gcc:12 AS builder
 
RUN wget "https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_linux_amd64.tar.gz" -O /tmp/seqkit.tar.gz && \
	tar zxvf /tmp/seqkit.tar.gz -C /usr/bin/ && \
	rm /tmp/seqkit.tar.gz
RUN git clone https://github.com/hyattpd/Prodigal.git && \
	cd Prodigal && \
	make install -j8
RUN wget "https://github.com/bbuchfink/diamond/releases/download/v2.0.8/diamond-linux64.tar.gz" -O /tmp/diamond-linux64.tar.gz && \
        tar zxvf /tmp/diamond-linux64.tar.gz -C /usr/bin/ && rm /tmp/diamond-linux64.tar.gz
RUN wget "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz" -O /tmp/ncbi-blast-2.10.1+-x64-linux.tar.gz && \
	mkdir /tmp/blast && \
        tar zxvf /tmp/ncbi-blast-2.10.1+-x64-linux.tar.gz -C /tmp/blast && \
	rm /tmp/ncbi-blast-2.10.1+-x64-linux.tar.gz
RUN git clone https://github.com/refresh-bio/kmer-db && \
	cd kmer-db && \
	make -j8
RUN wget "http://eddylab.org/software/infernal/infernal.tar.gz" -O /tmp/infernal.tar.gz && \
	tar zxvf /tmp/infernal.tar.gz -C /tmp && \
	cd /tmp/infernal-1.1.4 && \
	./configure --prefix /usr/bin/infernal && \
	make -j8 && \
	make check && \
	make install
RUN git clone https://github.com/DerrickWood/kraken2.git && \
	cd kraken2 && \
	./install_kraken2.sh /usr/bin/kraken2
FROM gcc:12
MAINTAINER iskoldt-X
COPY --from=builder /usr/bin/seqkit /usr/bin/
COPY --from=builder /usr/bin/diamond /usr/bin/
COPY --from=builder /usr/local/bin/prodigal /usr/local/bin/
COPY --from=builder /tmp/blast/ncbi-blast-2.10.1+ /usr/local/bin/blast
COPY --from=builder /kmer-db /usr/bin/kmer-db
COPY --from=builder /usr/bin/infernal /usr/bin/infernal
COPY --from=builder /usr/bin/kraken2 /usr/bin/kraken2
COPY . /
ENV TZ=Asia/Shanghai
RUN apt-get update && \
	DEBIAN_FRONTEND=nointeractive \
        apt-get install --no-install-suggests --no-install-recommends --yes\
        parallel hmmer libgomp1 python3 python3-pip && \
	apt-get clean && \
	pip install biopython && \
	export R_VERSION=4.2.0 && \
        wget "https://cran.rstudio.com/src/base/R-4/R-${R_VERSION}.tar.gz" -O /tmp/R-${R_VERSION}.tar.gz && \
        tar zxvf /tmp/R-${R_VERSION}.tar.gz -C /tmp && \
        cd /tmp/R-${R_VERSION} && \
        ./configure \
        --prefix=/opt/R \
        --enable-memory-profiling \
        --enable-R-shlib \
        --with-blas \
        --with-lapack && \
        make -j8 && \
        make install &&\
        ln -s /opt/R/bin/R /usr/local/bin/R && \
        ln -s /opt/R/bin/Rscript /usr/local/bin/Rscript && \
	cd / && \
	Rscript install.R
ENV PATH="/usr/bin/infernal/bin:/usr/bin/kraken2:/usr/bin/kmer-db:/usr/local/bin/blast/bin:/usr/bin/kmer-db:${PATH}"
CMD /scripts/Plasmer -h