diff --git a/containers/Dockerfile b/containers/Dockerfile
index f1b0a31b15e3ff868481553a5baa7c09a30c50a5..fe7c47feda57847ca65f64e41a2c82306b75fadd 100644
--- a/containers/Dockerfile
+++ b/containers/Dockerfile
@@ -1,137 +1,144 @@
-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
diff --git a/containers/Dockerfile-1.2.0 b/containers/Dockerfile-1.2.0
new file mode 100644
index 0000000000000000000000000000000000000000..fe7c47feda57847ca65f64e41a2c82306b75fadd
--- /dev/null
+++ b/containers/Dockerfile-1.2.0
@@ -0,0 +1,153 @@
+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']