jfroula/aligner-bbmap repository overview

FROM ubuntu:22.04

# Point to all the future conda installations you are going to do
ENV CONDAPATH=/usr/local/bin/miniconda3
ENV PATH=$CONDAPATH/bin:$PATH

# This will give us a workingdir within the container (e.g. a place we can mount data to)
WORKDIR /bbmap

# Install stuff with apt-get, and miniconda.
# There is a good reason to install miniconda in a path other than its default.
# The default intallation directory is /root/miniconda3 but this path will not be
# accessible by shifter or singularity so we'll install under /usr/local/bin/miniconda3.
RUN apt-get update && apt-get install -y wget bzip2 \
    && rm -rf /var/lib/apt/lists/* && \
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash ./Miniconda3*.sh -b -p $CONDAPATH \
    && rm Miniconda3*.sh && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge && \
    conda install bbmap==38.99 samtools==1.15.1 \
    && conda clean -afy

## Dockerfile
FROM ubuntu:22.04

# set DEBIAN_FRONTEND to noninteractive so you don't get prompted by 
# time zone questions during installation of git-all
ENV DEBIAN_FRONTEND noninteractive

# Install stuff with apt-get
RUN apt-get update && apt-get install -y wget bzip2 git-all \
    && rm -rf /var/lib/apt/lists/*

# Point to all the future conda installations you are going to do
ENV CONDAPATH=/usr/local/bin/miniconda3
ENV PATH=$CONDAPATH/bin:$PATH

# Install miniconda
# There is a good reason to install miniconda in a path other than its default.
# The default intallation directory is /root/miniconda3 but this path will not be
# accessible by shifter or singularity so we'll install under /usr/local/bin/miniconda3.
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh \
    && bash ./Miniconda3*.sh -b -p $CONDAPATH \
    && rm Miniconda3*.sh

# Install software with conda
RUN conda install -c bioconda bbmap==38.84 samtools==1.11 \
    && conda clean -afy

# This will give us a workingdir within the container (e.g. a place we can mount data to)
WORKDIR /bbmap

# Move script into container.
# Notes that it is copied to a location in your $PATH
RUN git clone https://gitlab.com/jgi-doe/jaws-workshop.git \
	&& mv jaws-workshop/workshop-8.18.22/script.sh /usr/local/bin/script.sh \
	&& rm -rf jaws-workshop \
        && chmod 755 /usr/local/bin/script.sh