diff --git a/containers/Dockerfile b/containers/Dockerfile index 2108283bf6a327e4faa1af61d898956ba7af4a55..16a3ca2704e96d926ec5bed6d531eb7c9f84378f 100644 --- a/containers/Dockerfile +++ b/containers/Dockerfile @@ -22,43 +22,43 @@ RUN pip3 install --upgrade pip # Update makeblastdb and blastp for prokka -WORKDIR /tmp +WORKDIR /install-dir RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ - cp /tmp/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\ - cp /tmp/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 /tmp +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 /tmp/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 /tmp +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 /tmp/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 /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln + rm -r /install-dir/barrnap-0.8/examples /install-dir/barrnap-0.8/build/*.aln # Install prodigal -WORKDIR /tmp +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 /tmp/Prodigal-2.6.3 +WORKDIR /install-dir/Prodigal-2.6.3 RUN make &&\ make install # Install prokka: -WORKDIR /tmp +WORKDIR /install-dir RUN apt-get install -y\ libdatetime-perl \ libxml-simple-perl \ @@ -67,77 +67,77 @@ RUN apt-get install -y\ default-jre \ bioperl RUN git clone https://github.com/tseemann/prokka.git -RUN /tmp/prokka/bin/prokka --setupdb &&\ - ln -s /tmp/prokka/bin/prokka /usr/local/bin +RUN /install-dir/prokka/bin/prokka --setupdb &&\ + ln -s /install-dir/prokka/bin/prokka /usr/local/bin # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e -WORKDIR /tmp +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 /tmp/mmseqs/bin/mmseqs /usr/local/bin &&\ + mv /install-dir/mmseqs/bin/mmseqs /usr/local/bin &&\ # remove useless files - rm -r /tmp/mmseqs + rm -r /install-dir/mmseqs # Install mafft 7.313 RUN rm /usr/bin/mafft # remove mafft installed with bioperl -WORKDIR /tmp +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 /tmp/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 /tmp +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 /tmp/FastTreeMP /usr/local/bin + ln -s /install-dir/FastTreeMP /usr/local/bin ## Install FastME FastME 2.1.6.1 -WORKDIR /tmp +WORKDIR /install-dir RUN apt-get install -y automake &&\ git clone https://gite.lirmm.fr/atgc/FastME.git -WORKDIR /tmp/FastME +WORKDIR /install-dir/FastME RUN ./configure &&\ make &&\ make install # Install quicktree -WORKDIR /tmp +WORKDIR /install-dir RUN git clone https://github.com/tseemann/quicktree WORKDIR quicktree RUN make &&\ - ln -s /tmp/quicktree/quicktree /usr/local/bin + ln -s /install-dir/quicktree/quicktree /usr/local/bin # Install iqtree -WORKDIR /tmp +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 /tmp/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 /tmp +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 /tmp/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 -WORKDIR /tmp +WORKDIR /install-dir RUN git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git -WORKDIR /tmp/pipeline_annotation +WORKDIR /install-dir/pipeline_annotation RUN git checkout dev &&\ ./make