Dockerfile.seqpipe

ARG REGISTRY=""
ARG BASE_IMAGE_TAG=latest
FROM ${REGISTRY}iossifovlab-mamba-base:${BASE_IMAGE_TAG}
# FROM condaforge/mambaforge:latest

ARG SOURCE_DIR="."


ADD ${SOURCE_DIR}/environment.yml /
ADD ${SOURCE_DIR}/dev-environment.yml /

RUN /opt/conda/bin/mamba env create --name gpf --file /environment.yml
RUN /opt/conda/bin/mamba env update --name gpf --file /dev-environment.yml

# GPF ENV
ENV PATH /opt/conda/envs/gpf/bin:$PATH

# HADOOP CONFIG
ENV JAVA_HOME /opt/conda/envs/gpf
ENV HADOOP_HOME /opt/conda/envs/gpf
ENV HADOOP_CONF_DIR /opt/conda/envs/gpf/etc/hadoop

RUN mkdir -p /data && mkdir -p /code

ENV DAE_DB_DIR "/data"

WORKDIR /code

SHELL ["/bin/bash", "-c"]