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Dockerfile
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FROM ubuntu:18.04 as blastbuild
ARG version
ARG num_procs=8
LABEL Description="NCBI BLAST" Vendor="NCBI/NLM/NIH" Version=${version} Maintainer=camacho@ncbi.nlm.nih.gov
USER root
WORKDIR /root/
RUN apt-get -y -m update && apt-get install -y build-essential curl libidn11 libnet-perl perl-doc liblmdb-dev
RUN curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}alpha/ncbi-blast-${version}-alpha+-src.tar.gz | \
tar xzf - && \
cd ncbi-blast-${version}+-src/c++ && \
./configure --with-optimization --with-dll --with-experimental=Int8GI --with-flat-makefile --with-openmp --prefix=/blast && \
cd ReleaseMT/build && \
make -j ${num_procs} -f Makefile.flat blastdb_aliastool.exe blastdbcheck.exe blastdbcmd.exe blast_formatter.exe blastn.exe blastp.exe blastx.exe convert2blastmask.exe deltablast.exe dustmasker.exe makeblastdb.exe makembindex.exe makeprofiledb.exe psiblast.exe rpsblast.exe rpstblastn.exe segmasker.exe tblastn.exe tblastx.exe windowmasker.exe
FROM ubuntu:18.04
ARG version
COPY VERSION .
USER root
WORKDIR /root/
RUN apt-get -y -m update && apt-get install -y libgomp1 libnet-perl libxml-simple-perl libjson-perl perl-doc liblmdb-dev parallel vmtouch cpanminus curl && rm -rf /var/lib/apt/lists/* && cpanm HTML::Entities
RUN mkdir -p /blast/bin /blast/lib
COPY --from=blastbuild /root/ncbi-blast-${version}+-src/c++/ReleaseMT/bin /blast/bin
COPY --from=blastbuild /root/ncbi-blast-${version}+-src/c++/ReleaseMT/lib /blast/lib
COPY --from=ncbi/edirect /usr/local/ncbi/edirect /root/edirect
RUN mkdir -p /blast/blastdb /blast/blastdb_custom
RUN sed -i '$ a BLASTDB=/blast/blastdb:/blast/blastdb_custom' /etc/environment
ENV BLASTDB /blast/blastdb:/blast/blastdb_custom
ENV PATH="/root/edirect:/blast/bin:${PATH}"
RUN curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/update_blastdb.pl -o update_blastdb.pl && install -m 755 update_blastdb.pl /blast/bin/ && rm -f update_blastdb.pl
RUN curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/blastdb_path -o /blast/bin/blastdb_path && chmod +x /blast/bin/blastdb_path && \
cp /blast/bin/blastp /blast/bin/blastp.REAL && \
curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/blastp.sh -o /blast/bin/blastp && chmod +x /blast/bin/blastp && \
cp /blast/bin/blastn /blast/bin/blastn.REAL && \
curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/blastn.sh -o /blast/bin/blastn && chmod +x /blast/bin/blastn && \
cp /blast/bin/blastx /blast/bin/blastx.REAL && \
curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/blastx.sh -o /blast/bin/blastx && chmod +x /blast/bin/blastx && \
cp /blast/bin/tblastn /blast/bin/tblastn.REAL && \
curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/tblastn.sh -o /blast/bin/tblastn && chmod +x /blast/bin/tblastn && \
cp /blast/bin/tblastx /blast/bin/tblastx.REAL && \
curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/temp/tblastx.sh -o /blast/bin/tblastx && chmod +x /blast/bin/tblastx
RUN echo 'will cite' | parallel --citation
WORKDIR /blast
CMD ["/bin/bash"]