Dockerfile.worker

FROM ncbi/sra-tools:x86_64-3.0.0 AS build-sra-tools

# https://github.com/renoki-co/laravel-docker-base
FROM quay.io/renokico/laravel-base:worker-1.2.0-8.0-cli-alpine

RUN apk --update add bash procps graphviz openjdk11-jre python3 && \
    rm -rf /var/cache/apk/*

COPY --from=build-sra-tools /usr/local/bin /usr/local/bin
COPY --from=build-sra-tools /root/.ncbi /root/.ncbi

# install parallel-fastq-dump
RUN wget -q -O parallel-fastq-dump.0.6.7.tar.gz https://github.com/rvalieris/parallel-fastq-dump/archive/refs/tags/0.6.7.tar.gz && \
  tar xzvf parallel-fastq-dump.0.6.7.tar.gz && cd parallel-fastq-dump-0.6.7 && \
  chmod +x parallel-fastq-dump && cp parallel-fastq-dump /usr/local/bin/ && \
  rm -rf ../parallel-fastq-dump.0.6.7.tar.gz ../parallel-fastq-dump-0.6.7

# install nextflow
ENV NXF_VER 22.10.8
RUN mkdir /opt/nextflow && cd /opt/nextflow && \
    curl -s https://get.nextflow.io | bash && \
    ln -s /opt/nextflow/nextflow /usr/local/bin/nextflow

COPY --chown=www-data:www-data . /var/www/html

WORKDIR /var/www/html

ENTRYPOINT ["php", "-a"]