Dockerfile

FROM garcianacho/fhibase:v1
LABEL maintainer="Nacho Garcia <iggl@fhi.no>"
ENV qual 15
ENV noise 0.15
USER docker
RUN cd /home/docker \
    && wget \
    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && mkdir /home/docker/.conda \
    && bash Miniconda3-latest-Linux-x86_64.sh -b \
    && rm -f Miniconda3-latest-Linux-x86_64.sh \
    && conda config --add channels defaults \
    && conda config --add channels bioconda \
    && conda config --add channels conda-forge \
    && conda install ivar \
    && conda install -c bioconda samtools\
    && conda install -c bioconda seqkit \
    && conda update -n base -c defaults conda \
    && conda install -c bioconda bedtools \
    && conda install -c bioconda nextalign \
    && conda install -c bioconda bowtie2 \
    && conda install -c bioconda minimap2 \
    && conda create -n nextclade \
    && ln -s /home/docker/miniconda3/lib/libcrypto.so.1.1 /home/docker/miniconda3/lib/libcrypto.so.1.0.0    
RUN /bin/bash -c ". activate nextclade && \
    conda install -c bioconda nextclade && \
    nextclade dataset get --name 'sars-cov-2' --output-dir '/home/docker/nc_sars-cov-2'"
USER root 
RUN Rscript -e "install.packages(c('doSNOW', \
'progress','foreach','parallel', 'seqinr', 'doParallel', \
 'ggplot2',  'reshape2', 'ggpubr', 'readxl','tidyverse','writexl',\
  'remotes', 'data.table','digest', 'BiocManager', 'phylotools', 'umap','plotly','htmlwidgets'))"

RUN Rscript -e "remotes::install_github('davidsjoberg/ggsankey')"
USER docker
RUN conda create -n cutadaptenv cutadapt
USER root
RUN wget https://github.com/jgm/pandoc/releases/download/3.1.1/pandoc-3.1.1-1-amd64.deb && dpkg -i pandoc-3.1.1-1-amd64.deb
RUN apt-get update \
	&& apt-get install -y --no-install-recommends \
		gfortran \
        gcc-10
RUN rm /usr/bin/gcc /usr/bin/gcc-ar /usr/bin/gcc-nm /usr/bin/gcc-ranlib \
    && ln /usr/bin/gcc-nm-10 /usr/bin/gcc-nm \
    && ln /usr/bin/gcc-ar-10 /usr/bin/gcc-ar \
    && ln /usr/bin/gcc-10 /usr/bin/gcc \
    && ln /usr/bin/gcc-ranlib-10 /usr/bin/gcc-ranlib 
RUN apt-get update \
	&& apt-get install -y --no-install-recommends \
		libglpk-dev

RUN Rscript -e "install.packages(c('uwot','lubridate','stringr','igraph', 'ggnetwork', 'ape','trelliscopejs'))"
ENV kmer="0"
ENV mem="high_mem"
ENV start=1250
ENV end=2250
ENV M=1300
ENV m=500
ENV poi="auto"
ENV mode=d
ENV trim=0

RUN mkdir -p /Data /home/docker/CommonFiles
COPY CommonFiles/ /home/docker/CommonFiles/
RUN chmod -R +rwx /home/docker/CommonFiles/* \
    && chmod 777 /Data 
RUN chown docker /home/docker/CommonFiles/reference/*
RUN chmod 777 /home/docker/CommonFiles/reference/MSA_Refs.tsv.gz
RUN chown -R docker /home/docker/CommonFiles/reference
USER docker

RUN /bin/bash -c ". activate nextclade && \
   nextclade dataset get --name 'sars-cov-2' --output-dir '/home/docker/nc_sars-cov-2'"  

WORKDIR /Data
CMD ["sh", "-c", "/home/docker/CommonFiles/WWAnalysis.sh ${qual} ${noise} ${start} ${end} ${m} ${M} ${mode} ${trim} ${poi} ${kmer} ${mem}"]