Commit 4dcd2774 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

install tbl2asn after prokka

parent 169b3e03
Pipeline #46816 passed with stage
in 12 minutes and 27 seconds
......@@ -22,11 +22,6 @@ 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 tbl2asn (used by prokka)
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 dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
......@@ -46,6 +41,12 @@ 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
# install tbl2asn (used by prokka)
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
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
......
......@@ -54,11 +54,6 @@ RUN make &&\
make install
# install tbl2asn (used by prokka)
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 dependencies for prokka:
WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
......@@ -77,6 +72,11 @@ RUN echo yes | cpan Bio::Perl
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
# install tbl2asn (used by prokka)
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 MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
......
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