Failed attempt to run docker for deseq2

I'm trying to install Bioconductor's DESeq2 via a docker container, and based on a Biostars suggestion, I went with the following Dockerfile setup:

Dockerfile

FROM bioconductor/release_base2

# Helps clean up Docker images
RUN rm -rf /var/lib/apt/lists/*

ADD setup.R /tmp/

# invalidates cache every 24 hours
ADD http://master.bioconductor.org/todays-date /tmp/

RUN R -f /tmp/setup.R

setup.R

pkgs <- c(
    "IRanges",
    "GenomicRanges",
    "ggplot2",
    "dplyr",
    "optparse",
    "SummarizedExperiment",
    "S4Vectors"
    )

ap.db <- available.packages(contrib.url(BiocManager::repositories()))
ap <- rownames(ap.db)
fnd <- pkgs %in% ap
pkgs_to_install <- pkgs[fnd]

ok <- BiocManager::install(pkgs_to_install, update=FALSE, ask=FALSE) %in% rownames(installed.packages())

if (!all(fnd))
    message("Packages not found in a valid repository (skipped):\n  ",
            paste(pkgs[!fnd], collapse="  \n  "))
if (!all(ok))
    stop("Failed to install:\n  ",
         paste(pkgs_to_install[!ok], collapse="  \n  "))

suppressWarnings(BiocManager::install(update=TRUE, ask=FALSE))

When I try to run this container interactively though, I get this response:

sudo docker run -v /home/ec2-user/data/:/data -it 096401932500.dkr.ecr.us-west-2.amazonaws.com/deseq2:dev
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] add: executing... 
Nothing additional to add
[cont-init.d] add: exited 0.
[cont-init.d] userconf: executing... 

ERROR: You must set a unique PASSWORD (not 'rstudio') first! e.g. run with:
docker run -e PASSWORD=<YOUR_PASS> -p 8787:8787 rocker/rstudio

Is there a better approach? Also, I want to be able to install python packages within the dockerfile (as I will be running this container on a python-based pipeline) - how can I properly conduct a multi-stage build to do so? I tried doing the following for this, but then my invoked python script run_deseq2.py responded with: /bin/sh: 1: Rscript: not found:

FROM bioconductor/release_base2

ADD src/setup.R /
RUN Rscript /setup.R 

ENV PATH=/usr/local/bin/:$PATH

FROM ubuntu:19.04 

ENV DEBIAN_FRONTEND=noninteractive  

WORKDIR / 

RUN apt-get update && \ 
    apt-get install -y \ 
        python-dev \ 
        python-pip \ 
        wget 

RUN pip install awscli boto3

COPY src/run_deseq2.py /
COPY src/s3_utils.py /
COPY src/job_utils.py /
COPY src/deseq2.R /
COPY src/ModelLoxTag.R /

ENV PATH=$PATH:~/.local/bin/ 
ENV R_THREADS=30 

# Run docker, starting with run script
ENTRYPOINT ["python", "/run_deseq2.py"]

Bioconductor / bioc_docker

Failed attempt to run docker for deseq2 #96