Dockerfile.bacteria_cloud

# syntax=docker/dockerfile:1
FROM {{{ imagebuilder:parentImage }}}
{{{ imagebuilder:environments }}}
{{{ imagebuilder:components }}}

WORKDIR /root/Snakemake

SHELL ["/bin/bash", "--login", "-c"]
RUN apt update && apt install -y awscli unzip && rm -rf /var/lib/apt/lists/*


RUN conda install -n base -c conda-forge mamba
RUN conda create --name bacterial 
RUN conda clean -afy && conda init bash 
RUN printf "conda activate bacterial" >> ~/.bashrc
RUN conda install -c conda-forge bioconda::snakemake=7.24.2

# getting the zip file from the EC2 instance
# the zip file is uploaded manually
# RUN wget http://bacteria-snakemake-provision


# RUN wget https://github.com/candress/snakemake-bacterial-whole-genome-pipeline/archive/refs/heads/main.zip
# RUN unzip snakemake-bacterial-whole-genome-pipeline-main.zip

RUN wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.10/sratoolkit.3.0.10-ubuntu64.tar.gz
RUN tar -xvf sratoolkit.3.0.10-ubuntu64.tar.gz
# OR
# not this one because it affects the next command:
# RUN wget --output-document sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
# RUN tar -vxzf sratoolkit.tar.gz


RUN sratoolkit.3.0.10-ubuntu64/bin/prefetch -p SRR24437709 SRR24437710 SRR24437713 SRR24437715
RUN sratoolkit.3.0.10-ubuntu64/bin/fastq-dump --gzip --split-3 SRR24437709/SRR24437709.sra SRR24437710/SRR24437710.sra SRR24437713/SRR24437713.sra SRR24437715/SRR24437715.sra

RUN rm -r SRR24437709 SRR24437710 SRR24437713 SRR24437715 sratoolkit.3.0.10-ubuntu64 sratoolkit.3.0.10-ubuntu64.tar.gz

RUN mv SRR24437709_1.fastq.gz SRR24437709_R1_001.fastq.gz
RUN mv SRR24437709_2.fastq.gz SRR24437709_R2_001.fastq.gz
RUN mv SRR24437710_1.fastq.gz SRR24437710_R1_001.fastq.gz
RUN mv SRR24437710_2.fastq.gz SRR24437710_R2_001.fastq.gz
RUN mv SRR24437713_1.fastq.gz SRR24437713_R1_001.fastq.gz
RUN mv SRR24437713_2.fastq.gz SRR24437713_R2_001.fastq.gz
RUN mv SRR24437715_1.fastq.gz SRR24437715_R1_001.fastq.gz
RUN mv SRR24437715_2.fastq.gz SRR24437715_R2_001.fastq.gz
RUN mkdir fastq
RUN mv SRR24437709_R1_001.fastq.gz SRR24437709_R2_001.fastq.gz SRR24437710_R1_001.fastq.gz SRR24437710_R2_001.fastq.gz SRR24437713_R1_001.fastq.gz SRR24437713_R2_001.fastq.gz SRR24437715_R1_001.fastq.gz SRR24437715_R2_001.fastq.gz fastq

RUN mv fastq snakemake-bacterial-whole-genome-pipeline-main

WORKDIR /root/Snakemake/snakemake-bacterial-whole-genome-pipeline-main

RUN snakemake --use-conda --conda-create-envs-only --cores 12

# this might cause an issue becasue the snakemake folder in mnt/efs/snakemake is mounted to the EC2 instance. It might be that this needs to be performed after running the docker image and loging in
# RUN cp -r /root/Snakemake/snakemake-bacterial-whole-genome-pipeline-main /mnt/efs/snakemake/

CMD /bin/bash


# still need to move these zip files to an apporopriate location AND test the pipeline (SRA directory not used)
# How to run the pipeline (take out slurm params)
# snakemake \
#     --jobs 64 \
#     --use-conda \
#     --rerun-incomplete \
#     --forceall \
#     --latency-wait 10 \