add updated dockerfile

containers/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\
     apt-get -y upgrade
 
-# Avec ubuntu 16.04, ajouter
-# apt install software-properties-common
-# add-apt-repository ppa:deadsnakes/ppa
-# apt-get update
-# apt-get install python3.6
-
-
 
 # Install packages needed and update pip
 RUN apt-get install -y \
         wget \
         python3 \
-        python3-pip
+        python3-pip \
+        git
 # Upgrade pip
 RUN pip3 install --upgrade pip
+RUN mkdir /install_dir
 
 
-# Update makeblastdb and blastp for prokka, with blast+ version 2.10.1
-WORKDIR /install-dir
+# Update makeblastdb and blastp for prokka
+WORKDIR /install_dir
 RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
     tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
-    cp /install-dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
-    cp /install-dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
+    cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
+    cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
     rm ncbi-blast-2.10.1+-x64-linux.tar.gz
 
 
 # Install mash
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
     tar -xf mash-Linux64-v2.2.tar &&\
     rm mash-Linux64-v2.2.tar &&\
-    mv /install-dir/mash-Linux64-v2.2/mash /usr/local/bin &&\
+    mv /install_dir/mash-Linux64-v2.2/mash /usr/local/bin &&\
     rm -r mash-Linux64-v2.2
 
 
 # Install barrnap
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
     tar -xf 0.8.tar.gz &&\
     rm 0.8.tar.gz &&\
-    mv /install-dir/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
+    mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
     # Remove heavy useless files
-    rm -r /install-dir/barrnap-0.8/examples /install-dir/barrnap-0.8/build/*.aln
+    rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
+
 
 # Install prodigal
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\
     tar -xzf v2.6.3.tar.gz &&\
     rm v2.6.3.tar.gz
-WORKDIR /install-dir/Prodigal-2.6.3
+WORKDIR /install_dir/Prodigal-2.6.3
 RUN make &&\
     make install
 
-# Install prokka:
-WORKDIR /install-dir
-RUN apt-get install -y\
+
+# Install dependencies for prokka:
+WORKDIR /install_dir
+RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
         libdatetime-perl \
         libxml-simple-perl \
         libdigest-md5-perl \
-        git \
+        hmmer \
         default-jre \
         bioperl
+# Install hmmer
+RUN echo yes | cpan Bio::SearchIO::hmmer
+# Install bioperl
+RUN echo yes | cpan Bio::Perl
+
+# Install prokka
 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
+RUN /install_dir/prokka/bin/prokka --setupdb &&\
+    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
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
     tar xvfz mmseqs-linux-sse41.tar.gz &&\
     rm mmseqs-linux-sse41.tar.gz &&\
-    mv /install-dir/mmseqs/bin/mmseqs /usr/local/bin &&\
+    mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
     # remove useless files
-    rm -r /install-dir/mmseqs
+    rm -r /install_dir/mmseqs
 
 
 # Install mafft 7.313
 RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\
     tar xf mafft-7.313-with-extensions-src.tgz &&\
     rm mafft-7.313-with-extensions-src.tgz
-WORKDIR /install-dir/mafft-7.313-with-extensions/core
+WORKDIR /install_dir/mafft-7.313-with-extensions/core
 RUN make clean &&\
     make &&\
     make install
 
 
 # Install FastTree version 2.1.11 Double precision (No SSE3)
-WORKDIR /install-dir
+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
-WORKDIR /install-dir
+# Install FastME FastME 2.1.6.1
+WORKDIR /install_dir
 RUN apt-get install -y automake  &&\
     git clone https://gite.lirmm.fr/atgc/FastME.git
-WORKDIR /install-dir/FastME
-RUN ./configure &&\
-    make &&\
-    make install
-
+WORKDIR /install_dir/FastME/tarball
+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
+WORKDIR /install_dir
 RUN git clone https://github.com/tseemann/quicktree
-WORKDIR quicktree
+WORKDIR /install_dir/quicktree
 RUN make &&\
-    ln -s /install-dir/quicktree/quicktree /usr/local/bin
+    ln -s /install_dir/quicktree/quicktree /usr/local/bin
 
 
 # Install iqtree
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
 RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
     rm iqtree-1.6.12-Linux.tar.gz &&\
-    ln -s /install-dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
+    ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
 
 
 # Install iqtree2
-WORKDIR /install-dir
+WORKDIR /install_dir
 RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
 RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
     rm iqtree-2.0.6-Linux.tar.gz &&\
-    ln -s /install-dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
+    ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
 
 
 # Install PanACoTA

containers/Dockerfile-1.2.0

+from ubuntu:20.04
+
+# Update apt-get packages
+RUN apt-get update &&\
+    apt-get -y upgrade
+
+
+# Install packages needed and update pip
+RUN apt-get install -y \
+        wget \
+        python3 \
+        python3-pip \
+        git
+# Upgrade pip
+RUN pip3 install --upgrade pip
+RUN mkdir /install_dir
+
+
+# Update makeblastdb and blastp for prokka
+WORKDIR /install_dir
+RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
+    tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
+    cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
+    cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
+    rm ncbi-blast-2.10.1+-x64-linux.tar.gz
+
+
+# Install mash
+WORKDIR /install_dir
+RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
+    tar -xf mash-Linux64-v2.2.tar &&\
+    rm mash-Linux64-v2.2.tar &&\
+    mv /install_dir/mash-Linux64-v2.2/mash /usr/local/bin &&\
+    rm -r mash-Linux64-v2.2
+
+
+# Install barrnap
+WORKDIR /install_dir
+RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
+    tar -xf 0.8.tar.gz &&\
+    rm 0.8.tar.gz &&\
+    mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
+    # Remove heavy useless files
+    rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
+
+
+# Install prodigal
+WORKDIR /install_dir
+RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\
+    tar -xzf v2.6.3.tar.gz &&\
+    rm v2.6.3.tar.gz
+WORKDIR /install_dir/Prodigal-2.6.3
+RUN make &&\
+    make install
+
+
+# Install dependencies for prokka:
+WORKDIR /install_dir
+RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
+        libdatetime-perl \
+        libxml-simple-perl \
+        libdigest-md5-perl \
+        hmmer \
+        default-jre \
+        bioperl
+# Install hmmer
+RUN echo yes | cpan Bio::SearchIO::hmmer
+# Install bioperl
+RUN echo yes | cpan Bio::Perl
+
+# Install prokka
+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
+# 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
+WORKDIR /install_dir
+RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
+    tar xvfz mmseqs-linux-sse41.tar.gz &&\
+    rm mmseqs-linux-sse41.tar.gz &&\
+    mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
+    # remove useless files
+    rm -r /install_dir/mmseqs
+
+
+# Install mafft 7.313
+RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
+WORKDIR /install_dir
+RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\
+    tar xf mafft-7.313-with-extensions-src.tgz &&\
+    rm mafft-7.313-with-extensions-src.tgz
+WORKDIR /install_dir/mafft-7.313-with-extensions/core
+RUN make clean &&\
+    make &&\
+    make install
+
+
+# Install FastTree version 2.1.11 Double precision (No SSE3)
+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
+
+
+# Install FastME FastME 2.1.6.1
+WORKDIR /install_dir
+RUN apt-get install -y automake  &&\
+    git clone https://gite.lirmm.fr/atgc/FastME.git
+WORKDIR /install_dir/FastME/tarball
+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
+WORKDIR /install_dir/quicktree
+RUN make &&\
+    ln -s /install_dir/quicktree/quicktree /usr/local/bin
+
+
+# Install iqtree
+WORKDIR /install_dir
+RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
+RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
+    rm iqtree-1.6.12-Linux.tar.gz &&\
+    ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
+
+
+# Install iqtree2
+WORKDIR /install_dir
+RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
+RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
+    rm iqtree-2.0.6-Linux.tar.gz &&\
+    ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
+
+
+# Install PanACoTA
+WORKDIR /install-dir
+RUN git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
+WORKDIR /install-dir/pipeline_annotation
+RUN git checkout master
+RUN ./make
+
+
+ENTRYPOINT ["/usr/local/bin/PanACoTA"]
+CMD ['-h']