#FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
FROM rust:1.61

USER root

SHELL ["/bin/bash", "-c"]
#SHELL [ "/bin/sh", "-s", ".", "$HOME/.cargo/env" ]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update -y && apt-get install -y software-properties-common --no-install-recommends \
    build-essential \
    cmake \
    curl \
    git \
    wget \
    ca-certificates \
    libopenblas-dev \
    libgsl-dev \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*

# Get Rust
#RUN curl https://sh.rustup.rs -sSf | bash -s -- --default-toolchain nightly -y 
#RUN source $HOME/.cargo/env
#RUN echo 'source $HOME/.cargo/env' >> $HOME/.bashrc 

# Install vcf2prot
RUN git clone https://github.com/ikmb/vcf2prot.git
WORKDIR /home/omic/vcf2prot

RUN cargo build --release 
 
WORKDIR /home/omic/vcf2prot/target/release

RUN export DEBUG_CPU_EXEC=TRUE
RUN export INSPECT_TXP=TRUE
RUN export INSPECT_INS_GEN=TRUE

#Test
RUN ./vcf2prot -h

WORKDIR /home/omic/vcf2prot
RUN gunzip examples/reference_sequences.fasta.gz

COPY reference.fasta .

#install bcftools
WORKDIR /home/omic/

# install conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
  mkdir -p /opt && \     
  bash miniconda.sh -b -p /opt/conda && \      
  rm miniconda.sh && \
  ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
  echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
  echo "conda activate base" >> ~/.bashrc && \
  find /opt/conda/ -follow -type f -name '*.a' -delete && \
  find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
  /opt/conda/bin/conda clean -afy

ENV PATH /opt/conda/bin:$PATH

## update conda
RUN conda update -y -n base -c defaults conda

# main conda env (vcf2prot)
RUN conda create -n vcf2prot python=3.9
ENV PATH "$PATH:/opt/conda/envs/vcf2prot/bin"
RUN echo "source activate vcf2prot" >> ~/.bashrc

RUN conda install -y -n vcf2prot -c bioconda openssl
RUN conda install -y -n vcf2prot -c conda-forge libgcc-ng
RUN conda install -y -n vcf2prot -c bioconda bcftools==1.20

#Install beagle
#RUN wget https://faculty.washington.edu/browning/beagle/beagle.28Jun21.220.jar

#Get data
RUN wget https://ftp.ensembl.org/pub/release-112/gff3/homo_sapiens/Homo_sapiens.GRCh38.112.gff3.gz
RUN gunzip Homo_sapiens.GRCh38.112.gff3.gz
#RUN wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
#RUN gunzip hg38.fa.gz
RUN wget https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
RUN gunzip Homo_sapiens.GRCh38.dna.toplevel.fa.gz

WORKDIR /home/omic/vcf2prot


RUN conda install -y -n vcf2prot numpy pandas


COPY MANE_transcipts_reference.fasta .