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FROM ubuntu:18.04
USER root
WORKDIR /root/
RUN apt-get -y -m update && apt-get install -y build-essential wget libidn11 libnet-perl liblist-moreutils-perl perl-doc libnet-ssleay-perl libcam-pdf-perl cpanminus libgomp1 python3-minimal python-pip
RUN cpanm IO::Socket::SSL \
LWP::Protocol::https \
Config::Simple \
Readonly \
HTML::Entities \
List::MoreUtils
##RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.7.1+-src.tar.gz
##RUN tar xvzf ncbi-blast-2.7.1+-src.tar.gz
##WORKDIR /root/ncbi-blast-2.7.1+-src/c++
##RUN ./configure --with-optimization --with-dll --with-experimental=Int8GI --with-flat-makefile --prefix=/blast
##WORKDIR /root/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build
##RUN make -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
##RUN mkdir -p /blast/bin /blast/lib
##COPY --from=blastbuild /root/ncbi-blast-2.7.1+-src/c++/ReleaseMT/bin /blast/bin
##COPY --from=blastbuild /root/ncbi-blast-2.7.1+-src/c++/ReleaseMT/lib /blast/lib
# BLAST Build is cumbersome and we will probably use 2.8 anyway. Just install from binary for now
## you need an updateable solution for this
RUN wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
RUN tar xvzf https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
ENV PATH="/sratoolkit.2.9.2-ubuntu64/bin:${PATH}"
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/ncbi-magicblast-1.4.0-x64-linux.tar.gz
RUN tar xvzf ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/ncbi-magicblast-1.4.0-x64-linux.tar.gz
ENV PATH="/ncbi-magicblast-1.4.0/bin:${PATH}"
RUN pip install pybedtools
ENV NAMEH htslib
ENV ENV NAME "samtools"
RUN git clone https://github.com/samtools/htslib.git && \
cd ${NAMEH} && \
## git reset --hard ${SHA1H} && \
make -j 4 && \
cd .. && \
cp ./${NAMEH}/tabix /usr/local/bin/ && \
cp ./${NAMEH}/bgzip /usr/local/bin/ && \
cp ./${NAMEH}/htsfile /usr/local/bin/ && \
strip /usr/local/bin/tabix; true && \
strip /usr/local/bin/bgzip; true && \
strip /usr/local/bin/htsfile; true &&
RUN git clone https://github.com/samtools/samtools.git && \
cd ${NAME} && \
## git reset --hard ${SHA1} && \
make -j 4 && \
cp ./${NAME} /usr/local/bin/ && \
cd .. && \
strip /usr/local/bin/${NAME}; true && \
rm -rf ./${NAMEH}/ && \
rm -rf ./${NAME}/ && \
rm -rf ./${NAMEH}
RUN wget ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz
RUN tar -xvzf edirect.tar.gz
RUN bash ./edirect/setup.sh
ENV PATH="/edirect/bin:${PATH}"
## this will need to be updated
RUN wget http://eddylab.org/software/hmmer/hmmer.tar.gz
RUN tar -xvzf hmmer.tar.gz && \
cd hmmer-3.2.1 && \
./configure && \
make && \
make install
## Packages that still need to be installed
# Skesa
## Conda (PIA)
## this may be helpful: https://mfr.osf.io/render?url=https://osf.io/tf2mn/?action=download%26mode=render
WORKDIR /blast/blastdb
ENV BLASTDB /blast/blastdb
ENV PATH="/blast/bin:${PATH}"
CMD ["/bin/bash"]