Dockerfile

FROM ubuntu:xenial

LABEL base.image="ubuntu:xenial"
LABEL dockerfile.version="1"
LABEL software="BBTools"
LABEL software.version="38.86"
LABEL description="A set of tools labeled as \"Bestus Bioinformaticus\""
LABEL website="https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
LABEL license="https://jgi.doe.gov/disclaimer/"
LABEL maintainer="Abigail Shockey"
LABEL maintainer.email="abigail.shockey@slh.wisc.edu"

RUN apt-get update && apt-get install -y build-essential \
  openjdk-8-jre-headless \
  wget \
  samtools

# get miniconda and the artic-ncov19 repo
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
  bash ./Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b  && \
  rm Miniconda3-latest-Linux-x86_64.sh

# set the environment
ENV PATH="/miniconda/bin:$PATH"

RUN conda config --add channels defaults && \
  conda config --add channels bioconda && \
  conda config --add channels conda-forge && \
  conda install sambamba

RUN wget https://sourceforge.net/projects/bbmap/files/BBMap_38.86.tar.gz && \
  tar -xzf BBMap_38.86.tar.gz && \
  rm BBMap_38.86.tar.gz

ENV PATH="${PATH}:/bbmap"\
 LC_ALL=C

WORKDIR /data