Dockerfile

FROM nfcore/base
LABEL authors="Qi Zhao" \
      description="Docker image containing all requirements for nf-core/multiexseq pipeline"

COPY environment1.yml environment2.yml ./

RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz && tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz

ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH
RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a

ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH
RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a

RUN cd annovar \
    #&& echo "./opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
    #&& echo "conda activate" >> ~/.bashrc \
    #&& conda activate multiexseq_freec \
    && perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/

# ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH

CMD ["/bin/bash"]