diff --git a/dockerfile/dockerfile b/dockerfile/dockerfile new file mode 100644 index 0000000..1e65c09 --- /dev/null +++ b/dockerfile/dockerfile @@ -0,0 +1,46 @@ +FROM ubuntu:22.04 +RUN apt update && apt upgrade -y +RUN apt install -y wget +RUN wget https://repo.anaconda.com/archive/Anaconda3-2024.06-1-Linux-x86_64.sh +RUN bash Anaconda3-2024.06-1-Linux-x86_64.sh -b -p $HOME/anaconda3 +RUN ~/anaconda3/bin/conda init +RUN wget https://github.com/marbl/Mash/releases/download/v2.3/mash-Linux64-v2.3.tar +RUN tar -xvf mash-Linux64-v2.3.tar +RUN mv mash-Linux64-v2.3/mash /usr/local/bin +RUN rm -rf mash-Linux64-v2.3.tar mash-Linux64-v2.3 +RUN /root/anaconda3/bin/pip install drep +RUN apt-get install gcc -y +RUN apt-get install g++ -y +RUN apt-get install make -y +RUN apt install perl -y +RUN apt-get install csh -y +RUN wget https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download +RUN tar -xvf download +RUN cd MUMmer3.23 && make +ENV PATH="export PATH=$PATH:/MUMmer3.23/" +RUN apt install hmmer -y +RUN /root/anaconda3/bin/pip install checkm-genome +RUN /root/anaconda3/bin/conda install bioconda::prodigal +RUN /root/anaconda3/bin/conda install -c bioconda pplacer +RUN wget https://github.com/ParBLiSS/FastANI/releases/download/v1.34/fastANI-linux64-v1.34.zip +RUN apt install unzip -y +RUN unzip fastANI-linux64-v1.34.zip +RUN mv fastANI /usr/local/bin +RUN apt install -y git +RUN git clone https://github.com/abadona/qsimscan.git +RUN cd qsimscan && make +ENV PATH="export PATH=$PATH:/qsimscan/psimscan:/qsimscan/nsimscan" +RUN cd /root +RUN git clone https://github.com/DaehwanKimLab/centrifuge +RUN cd centrifuge && make +ENV PATH="export PATH=$PATH:/centrifuge/" +RUN mkdir skani_dir && cd skani_dir +RUN wget https://github.com/bluenote-1577/skani/releases/download/latest/skani +RUN chmod +x skani +RUN mv skani /usr/local/bin +RUN mkdir checkm_db && cd checkm_db +RUN wget https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz +RUN mv checkm_data_2015_01_16.tar.gz /checkm_db +RUN cd /checkm_db && tar -xvf checkm_data_2015_01_16.tar.gz +RUN rm /checkm_db/checkm_data_2015_01_16.tar.gz +ENV CHECKM_DATA_PATH="/checkm_db/"