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Commit 4dcd2774 authored by Amandine  PERRIN's avatar Amandine PERRIN
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install tbl2asn after prokka

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Pipeline #46816 passed
...@@ -22,11 +22,6 @@ RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2 ...@@ -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 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: # Install dependencies for prokka:
WORKDIR /install_dir WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
...@@ -46,6 +41,12 @@ RUN git clone https://github.com/tseemann/prokka.git ...@@ -46,6 +41,12 @@ RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\ RUN /install_dir/prokka/bin/prokka --setupdb &&\
ln -s /install_dir/prokka/bin/prokka /usr/local/bin 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 RUN rm /usr/bin/mafft # remove mafft installed with bioperl
......
...@@ -54,11 +54,6 @@ RUN make &&\ ...@@ -54,11 +54,6 @@ RUN make &&\
make install 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: # Install dependencies for prokka:
WORKDIR /install_dir WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
...@@ -77,6 +72,11 @@ RUN echo yes | cpan Bio::Perl ...@@ -77,6 +72,11 @@ RUN echo yes | cpan Bio::Perl
RUN git clone https://github.com/tseemann/prokka.git RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\ RUN /install_dir/prokka/bin/prokka --setupdb &&\
ln -s /install_dir/prokka/bin/prokka /usr/local/bin 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 # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
......
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