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dockerfile #241

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dockerfile
ParsaGhadermazi Oct 1, 2024
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ParsaGhadermazi Oct 1, 2024
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ParsaGhadermazi Oct 2, 2024
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46 changes: 46 additions & 0 deletions dockerfile/dockerfile
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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/"