diff --git a/containers/Dockerfile b/containers/Dockerfile index b9a640bfb1c958376f29887c1a275b7702346554..0919521b51dbb0abd0f338c29e4b5226e02bdbb0 100644 --- a/containers/Dockerfile +++ b/containers/Dockerfile @@ -28,10 +28,10 @@ RUN apt-get update &&\ # Install packages needed and update pip RUN apt-get install -y \ - wget \ - python3 \ - python3-pip \ - git + wget \ + python3 \ + python3-pip \ + git # Upgrade pip RUN pip3 install --upgrade pip RUN mkdir /install_dir @@ -70,7 +70,15 @@ RUN wget https://github.com/marbl/Mash/releases/download/${MASH_VER}/mash-Linux6 # gunzip tbl2asn.gz &&\ # chmod +x tbl2asn &&\ # ln -s /install_dir/tbl2asn /usr/local/bin -RUN apt-get install -y prokka +WORKDIR /install_dir +# RUN apt-get install -y prokka +# RUN git clone https://github.com/tseemann/prokka.git +# RUN prokka --dbdir /install_dir/prokka/db/ --setupdb +# RUN prokka +# RUN prokka --setupdb +# RUN mv /usr/bin/prokka /usr/bin/prokka-apt +# RUN echo "alias 'prokka'='/install_dir/prokka/bin/prokka'" > ~/.bash_aliases +# RUN source ~/.bashrc WORKDIR /install_dir # RUN DEBIAN_FRONTEND="noninteractive" apt install -y\ @@ -102,73 +110,73 @@ WORKDIR /install_dir # # ln -s /install_dir/tbl2asn /usr/local/bin # # more Examples/commands/2-Annotate.sh # # PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10 - -# Install prodigal -RUN apt-get install prodigal + +# # Install prodigal +# RUN apt-get install prodigal +# # WORKDIR /install_dir +# # RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\ +# # tar -xzf v${PRODIGAL_VER}.tar.gz &&\ +# # rm v${PRODIGAL_VER}.tar.gz +# # WORKDIR /install_dir/Prodigal-${PRODIGAL_VER} +# # RUN make +# # RUN make install + +# # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e # WORKDIR /install_dir -# RUN wget https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VER}.tar.gz &&\ -# tar -xzf v${PRODIGAL_VER}.tar.gz &&\ -# rm v${PRODIGAL_VER}.tar.gz -# WORKDIR /install_dir/Prodigal-${PRODIGAL_VER} -# RUN make -# RUN make install - -# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e -WORKDIR /install_dir -RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ - tar xvfz mmseqs-linux-sse41.tar.gz &&\ - rm mmseqs-linux-sse41.tar.gz &&\ - mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\ - # remove useless files - rm -r /install_dir/mmseqs - -# # Install mafft 7.313 -# RUN rm /usr/bin/mafft # remove mafft installed with bioperl +# RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ +# tar xvfz mmseqs-linux-sse41.tar.gz &&\ +# rm mmseqs-linux-sse41.tar.gz &&\ +# mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\ +# # remove useless files +# rm -r /install_dir/mmseqs + +# # # Install mafft 7.313 +# # RUN rm /usr/bin/mafft # remove mafft installed with bioperl +# # WORKDIR /install_dir +# # RUN wget https://mafft.cbrc.jp/alignment/software/mafft-${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) # 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) -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 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 @@ -177,5 +185,5 @@ RUN tar -xzf v${PANACOTA_VER}.tar.gz WORKDIR /install_dir/PanACoTA-${PANACOTA_VER} 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 diff --git a/containers/libncbi.so.6 b/containers/libncbi.so.6 new file mode 100644 index 0000000000000000000000000000000000000000..4c52357a06d0f73b22978d133caaa10d37cb5290 Binary files /dev/null and b/containers/libncbi.so.6 differ