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Commit 4368fd32 authored by Amandine  PERRIN's avatar Amandine PERRIN
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update prokka install for annote_and_1tree docker image

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Pipeline #46181 passed
...@@ -22,7 +22,7 @@ RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2 ...@@ -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 rm ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install 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\
libdatetime-perl \ libdatetime-perl \
...@@ -31,12 +31,22 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ ...@@ -31,12 +31,22 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
hmmer \ hmmer \
default-jre \ default-jre \
bioperl bioperl
# Install hmmer
RUN echo yes | cpan Bio::SearchIO::hmmer RUN echo yes | cpan Bio::SearchIO::hmmer
# Install bioperl
RUN echo yes | cpan Bio::Perl 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 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
RUN rm /usr/bin/mafft # remove mafft installed with bioperl RUN rm /usr/bin/mafft # remove mafft installed with bioperl
# Install quicktree # Install quicktree
......
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