Commit 3d1ad6a1 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

update prokka installation in docker image

- need to set 'yes' by default to install libxml-simple-perl library (RUN DEBIAN_FRONTEND="noninteractive" apt install)
- need to install bioperl from cpan (RUN echo yes | cpan Bio::Perl)
parent 97298a7a
Pipeline #43713 canceled with stage
in 4 minutes and 42 seconds
......@@ -30,6 +30,7 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
git \
default-jre \
bioperl
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
......
......@@ -16,7 +16,7 @@ RUN apt-get install -y \
RUN pip3 install --upgrade pip
# Install packages to install mafft
RUN apt-get install -y \
RUN DEBIAN_FRONTEND="noninteractive" apt-get install -y \
libdatetime-perl \
libxml-simple-perl \
libdigest-md5-perl \
......
......@@ -62,6 +62,7 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
git \
default-jre \
bioperl
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
......
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