diff --git a/containers/Dockerfile b/containers/Dockerfile
index 0919521b51dbb0abd0f338c29e4b5226e02bdbb0..509a7604e6b09bf4749799a2a0485571d33e0efc 100644
--- a/containers/Dockerfile
+++ b/containers/Dockerfile
@@ -72,10 +72,20 @@ RUN wget https://github.com/marbl/Mash/releases/download/${MASH_VER}/mash-Linux6
 #     ln -s /install_dir/tbl2asn /usr/local/bin
 WORKDIR /install_dir
 # RUN apt-get install -y prokka
-# RUN git clone https://github.com/tseemann/prokka.git
+RUN apt-get install -y libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl hmmer
+RUN git clone https://github.com/tseemann/prokka.git
+
+# Copy tbl2asn files from panacota repo
+RUN git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
+WORKDIR /install_dir/pipeline_annotation
+RUN git checkout dev
+RUN ln -s /install_dir/pipeline_annotation/containers/tbl2asn /usr/bin
+RUN ln -s /install_dir/prokka/bin/prokka /usr/bin
+RUN cp containers/lib* /lib/x86_64-linux-gnu/
 # RUN prokka --dbdir /install_dir/prokka/db/ --setupdb
 # RUN prokka
-# RUN prokka --setupdb
+RUN prokka --setupdb
+RUN cpan Bio::SearchIO::hmmer
 # RUN mv /usr/bin/prokka /usr/bin/prokka-apt
 # RUN echo "alias 'prokka'='/install_dir/prokka/bin/prokka'" > ~/.bash_aliases
 # RUN source ~/.bashrc
@@ -112,78 +122,80 @@ WORKDIR /install_dir
 # # PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
 
 
-# # Install prodigal
-# RUN apt-get install prodigal
-# # WORKDIR /install_dir
-# # RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\
-# #     tar -xzf v${PRODIGAL_VER}.tar.gz &&\
-# #     rm v${PRODIGAL_VER}.tar.gz
-# # WORKDIR /install_dir/Prodigal-${PRODIGAL_VER}
-# # RUN make 
-# # RUN make install
-
-# # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
+# Install prodigal
+RUN apt-get install prodigal
 # 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-${MAFFT_VER}-with-extensions-src.tgz &&\
-# #     tar xf mafft-7.313-with-extensions-src.tgz &&\
-# #     rm mafft-7.313-with-extensions-src.tgz
-# # WORKDIR /install_dir/mafft-7.313-with-extensions/core
-# # RUN make clean &&\
-# #     make &&\
-# #     make install
-
-# # # Install FastTree version 2.1.11 Double precision (No SSE3)
+# RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\
+#     tar -xzf v${PRODIGAL_VER}.tar.gz &&\
+#     rm v${PRODIGAL_VER}.tar.gz
+# WORKDIR /install_dir/Prodigal-${PRODIGAL_VER}
+# RUN make 
+# RUN make install
+
+# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
+WORKDIR /install_dir
+RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
+    tar xvfz mmseqs-linux-sse41.tar.gz &&\
+    rm mmseqs-linux-sse41.tar.gz &&\
+    mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
+    # remove useless files
+    rm -r /install_dir/mmseqs
+
+# # Install mafft 7.313
+# RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
 # WORKDIR /install_dir
-# RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
-#     gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
-#     ln -s /install_dir/FastTreeMP /usr/local/bin
+# RUN wget https://mafft.cbrc.jp/alignment/software/mafft-${MAFFT_VER}-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-2.1.6.4.tar.gz &&\
-#     rm fastme-2.1.6.4.tar.gz &&\
-#     ln -s /install_dir/FastME/tarball/fastme-2.1.6.4/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 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-2.1.6.4.tar.gz &&\
+    rm fastme-2.1.6.4.tar.gz &&\
+    ln -s /install_dir/FastME/tarball/fastme-2.1.6.4/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 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 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 wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/v${PANACOTA_VER}.tar.gz
-RUN tar -xzf v${PANACOTA_VER}.tar.gz
-WORKDIR /install_dir/PanACoTA-${PANACOTA_VER}
+# RUN wget https://github.com/gem-pasteur/PanACoTA/archive/refs/tags/v${PANACOTA_VER}.tar.gz
+# RUN tar -xzf v${PANACOTA_VER}.tar.gz
+RUN git clone https://github.com/gem-pasteur/PanACoTA.git
+# WORKDIR /install_dir/PanACoTA-${PANACOTA_VER}
+WORKDIR /install_dir/PanACoTA
 RUN ./make develop
 
-# ENTRYPOINT ["/usr/local/bin/PanACoTA"]
-# CMD ['-h']
\ No newline at end of file
+ENTRYPOINT ["/usr/local/bin/PanACoTA"]
+CMD ['-h']
\ No newline at end of file