Dockerfile

################## BASE IMAGE #####################
FROM continuumio/miniconda3:4.7.12

################## METADATA #######################
LABEL base_image="continuumio/miniconda3"
LABEL version="4.7.12"
LABEL software="Imputation-nf"
LABEL software.version="1.0"
LABEL about.summary="Container image containing all requirements for Imputation-nf"
LABEL about.home="http://github.com/IARCbioinfo/Imputation-nf"
LABEL about.documentation="http://github.com/IARCbioinfo/Imputation-nf/README.md"
LABEL about.license_file="http://github.com/IARCbioinfo/Imputation-nf/LICENSE.txt"
LABEL about.license="GNU-3.0"

################## INSTALLATION ######################
COPY environment.yml /
RUN apt-get update && apt-get install -y procps && apt-get clean -y
RUN conda env create -n Imputation-nf -f /environment.yml && conda clean -a
RUN apt-get install -y curl
RUN apt-get install -y unzip

RUN apt-get install -y cmake python-pip python-dev
RUN pip install cget 
RUN git clone https://github.com/statgen/Minimac4.git ; cd Minimac4 ; bash install.sh

RUN wget https://data.broadinstitute.org/alkesgroup/Eagle/downloads/Eagle_v2.4.1.tar.gz
RUN tar xvzf Eagle_v2.4.1.tar.gz
RUN rm Eagle_v2.4.1.tar.gz

RUN curl -sL imputationbot.now.sh | bash
RUN cp imputationbot /usr/local/bin
RUN cp imputationbot.jar /usr/local/bin

ENV PATH /opt/conda/envs/Imputation-nf/bin:$PATH
ENV PATH="$PATH:/Eagle_v2.4.1"
ENV PATH="$PATH:/Minimac4/release-build"