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Commit 26536521 authored by Amandine  PERRIN's avatar Amandine PERRIN
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install tbl2asn before bioperl and hmmer

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Pipeline #46185 passed
......@@ -22,6 +22,11 @@ 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\
......@@ -35,11 +40,6 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
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
......
......
......@@ -54,6 +54,11 @@ 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\
......@@ -67,11 +72,6 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
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
......
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