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# base image
FROM ubuntu:bionic
# metadata
LABEL base.image="ubuntu:bionic"
LABEL version="1"
LABEL software="staramr"
LABEL software.version="0.7.1"
LABEL description="staramr scans bacterial genome contigs for AMR genes and plasmids"
LABEL website="https://github.com/phac-nml/staramr"
LABEL license="https://github.com/phac-nml/staramr/blob/master/LICENSE"
LABEL maintainer1="Rachael St. Jacques"
LABEL maintainer1.email="[email protected]"
LABEL maintainer2="Curtis Kapsak"
LABEL maintainer2.email="[email protected]"
# install dependencies
RUN apt-get update && apt-get install -y \
python3 \
python3-pip \
git \
wget \
libmoo-perl \
liblist-moreutils-perl \
libjson-perl \
gzip \
file
# blast 2.9.0 (blast in apt for ubuntu:bionic is v2.6.0 from 2017)
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz && \
tar -xzf ncbi-blast-2.9.0+-x64-linux.tar.gz && \
rm ncbi-blast-2.9.0+-x64-linux.tar.gz
# any2fasta
RUN cd /usr/local/bin && \
wget https://raw.githubusercontent.com/tseemann/any2fasta/master/any2fasta && \
chmod +x any2fasta
# mlst 2.19.0
# apt dependencies: wget libmoo-perl liblist-moreutils-perl libjson-perl gzip file
# also requires blast 2.9.0 or greater
RUN wget https://github.com/tseemann/mlst/archive/v2.19.0.tar.gz && \
tar -xzf v2.19.0.tar.gz && \
rm v2.19.0.tar.gz
# staramr 0.7.1
# pandas 0.25.3 is a hard requirement at the moment. see here for more info: https://github.com/phac-nml/staramr/issues/115
RUN pip3 install staramr==0.7.1 pandas==0.25.3 && \
mkdir /data
# set $PATH and locale settings for singularity
ENV PATH="${PATH}:/mlst-2.19.0/bin:\
/ncbi-blast-2.9.0+/bin" \
LC_ALL=C
# update staramr default databases and print db info
RUN staramr db update -d && staramr db info
WORKDIR /data
##### staramr db information in container at time of docker image build #####
#resfinder_db_dir = /usr/local/lib/python3.6/dist-packages/staramr/databases/data/update/resfinder
#resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
#resfinder_db_commit = 7e1135b184abddea642fa2fd7c9322a33cb84810
#resfinder_db_date = Fri, 24 Apr 2020 11:11
#pointfinder_db_dir = /usr/local/lib/python3.6/dist-packages/staramr/databases/data/update/pointfinder
#pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
#pointfinder_db_commit = 6323b5cfa383805938672a60988a597544cf9914
#pointfinder_db_date = Fri, 30 Aug 2019 18:32
#plasmidfinder_db_dir = /usr/local/lib/python3.6/dist-packages/staramr/databases/data/update/plasmidfinder
#plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
#plasmidfinder_db_commit = acfd0096c01a4b03693b4a11374450f664d8d585
#plasmidfinder_db_date = Thu, 02 Apr 2020 11:42
#mlst_version = 2.19.0
#pointfinder_gene_drug_version = 050218
#resfinder_gene_drug_version = 050218.1