diff --git a/for_build/annote_and_1tree/Dockerfile b/for_build/annote_and_1tree/Dockerfile index 9418190537460cec9a9d2668c6fd8e6997d0c368..b57e7eade2d95e5a5ea3c666f09280e4d300a9c0 100644 --- a/for_build/annote_and_1tree/Dockerfile +++ b/for_build/annote_and_1tree/Dockerfile @@ -22,7 +22,7 @@ RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2 rm ncbi-blast-2.10.1+-x64-linux.tar.gz -# Install prokka: +# Install dependencies for prokka: WORKDIR /install_dir RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ libdatetime-perl \ @@ -31,12 +31,22 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ hmmer \ default-jre \ bioperl +# Install hmmer RUN echo yes | cpan Bio::SearchIO::hmmer +# Install bioperl RUN echo yes | cpan Bio::Perl +# install tbl2asn +RUN wget -O tbl2asn.gz ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz &&\ + gunzip tbl2asn.gz &&\ + chmod +x tbl2asn &&\ + ln -s /install_dir/tbl2asn /usr/local/bin + +# Install prokka RUN git clone https://github.com/tseemann/prokka.git RUN /install_dir/prokka/bin/prokka --setupdb &&\ ln -s /install_dir/prokka/bin/prokka /usr/local/bin + RUN rm /usr/bin/mafft # remove mafft installed with bioperl # Install quicktree