Commit e0c261ad authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

update prokka installation on ubuntu 20.04

parent d85cb0e6
Pipeline #46154 passed with stage
in 12 minutes and 6 seconds
......@@ -8,6 +8,7 @@ RUN apt-get update &&\
RUN apt-get install -y \
wget \
python3 \
git \
python3-pip
# Upgrade pip
RUN pip3 install --upgrade pip
......@@ -27,9 +28,9 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \
libxml-simple-perl \
libdigest-md5-perl \
git \
default-jre \
bioperl
RUN echo yes | cpan Bio::SearchIO::hmmer
RUN echo yes | cpan Bio::Perl
RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\
......
......@@ -9,7 +9,8 @@ RUN apt-get update &&\
RUN apt-get install -y \
wget \
python3 \
python3-pip
python3-pip \
git
# Upgrade pip
RUN pip3 install --upgrade pip
RUN mkdir /install_dir
......@@ -59,9 +60,9 @@ RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
libdatetime-perl \
libxml-simple-perl \
libdigest-md5-perl \
git \
default-jre \
bioperl
RUN echo yes | cpan Bio::SearchIO::hmmer
RUN echo yes | cpan Bio::Perl
RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\
......@@ -94,7 +95,7 @@ RUN make clean &&\
WORKDIR /install_dir
RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
ln -s /install_dir/FastTreeMP /usr/local/bin
ln -s /install_dir /FastTreeMP /usr/local/bin
# Install FastME FastME 2.1.6.1
......@@ -106,7 +107,6 @@ RUN tar xzf fastme-2.1.6.2.tar.gz &&\
rm fastme-2.1.6.2.tar.gz &&\
ln -s /install_dir/FastME/tarball/fastme-2.1.6.2/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme
# Install quicktree
WORKDIR /install_dir
RUN git clone https://github.com/tseemann/quicktree
......
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