Dockerfile

FROM continuumio/miniconda3:4.7.12 as build

ARG amrfinder_version=3.6.10

RUN apt-get --yes update && apt-get --yes upgrade && apt-get install --yes curl wget gzip unzip git && apt-get clean

RUN conda update conda

RUN conda install -c conda-forge -c bioconda -c defaults file blast=2.9=pl526h3066fca_4 ncbi-amrfinderplus=$amrfinder_version snakemake-minimal=5.8.2

RUN amrfinder -u

RUN cd /opt && mkdir -p abritamr

COPY . /opt/abritamr 

RUN cd /opt/abritamr && pip install .

RUN conda remove --force curl entrez-direct tqdm idna pip setuptools wheel asn1crypto ca-certificates cryptography expat chardet libcurl libedit libssh2 ncurses openssl conda-package-handling readline pysocks pycosats pycparser pyopenssl sqlite tk urllib3 requests yaml ruamel_yaml

RUN cd /opt/conda && rm -rf pkgs && rm -rf man/man* && cd bin && find * \( -iname "*blast*" -or -iname "*masker*" -or -iname "seqdb*" -or -iname "makembindex" \)  ! -iname "blastp" ! -iname "blastn" ! -iname "blastx" -type f -print -exec rm {} \;

FROM bitnami/minideb:buster

COPY --from=build /opt/conda /opt/conda

ENV PATH=/opt/conda/bin:$PATH

CMD [ "/bin/bash" ]