Dockerfile not correctly installing dependencies - docker

Question

I am having an issue with installing dependencies with a Dockerfile. The image builds successfully, but when I attempt to test some of the dependencies installed in the Dockerfile below, they do not seem to be found. I am new to creating Dockerfiles so I am not sure if I am missing something. This may having something to do with environment variables? For example, I install sl as a test to confirm that something is not right. When a access a shell of my running image, running 'sl' returns "Command not found". Please let me know what I am doing wrong.
Here is my Dockerfile that I am using to build an image:
#FROM specifies the parent image from which we will construct our own custom image. This tomcat image contains a limited dist of Ubuntu, Tomcat9, and JRE11 ("temurin" is just a limited version of Java)
FROM tomcat:9-jre11-temurin
#add a maintainer label to the image
LABEL maintainer="Kerrick Cavanaugh - kerrickcavanaugh#ufl.edu"
#SciPy, Pandas, Numpy, other deps
RUN apt-get update && \
yes | apt-get -qq -y install \
git \
build-essential \
software-properties-common \
# python-dev \
python3 \
python3-dev \
python-dev \
libssl-dev \
# libffi-dev \
libxml2-dev \
libxslt1-dev \
apt-utils \
zlib1g-dev \
pip \
python3-pip \
sl \
gfortran \
libopenblas-dev \
liblapack-dev \
wget
# add /root/.local/bin to python path (causing warnings)
RUN python3 -c "import sys; sys.path.append('/root/.local/bin');"
RUN pip3 install --upgrade pip && pip3 install -vvv \
wheel \
matplotlib \
ipython \
jupyter \
sympy \
cython \
et-xmlfile==1.0.1 \
imbalanced-learn==0.5.0 \
imblearn==0.0 \
jdcal==1.4.1 \
joblib==0.14.0 \
numpy==1.16.4 \
scipy==1.3.1 \
openpyxl==2.6.4 \
pandas==0.24.2 \
python-dateutil==2.8.0 \
pytest==4.6.3 \
pytest-cov==2.7.1 \
pytz==2019.3 \
scikit-learn==0.21.3 \
six==1.12.0 \
xlrd==1.2.0
#R
RUN apt update && echo 'Y' | apt upgrade && \
#removed sudo from next 4
echo 'Y' | apt install dirmngr gnupg apt-transport-https ca-certificates software-properties-common && \
echo 'Y' | apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
echo 'Y' | add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' && \
echo 'Y' | apt install r-base && \
R --version
#MATLAB???
#FSL
COPY ./aidp_docker/fslinstaller.py /usr/local/tomcat
#printf '36' | <-- for keyboard
#removed sudo
RUN apt-get update && apt-get -qq install python2
RUN { echo; echo '36'; } | python2 /usr/local/tomcat/fslinstaller.py -E -v -q > /dev/null
#AFNI
RUN cd && \
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_20_64_a_admin.txt && \
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_20_64_b_user.tcsh && \
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_20_64_c_nice.tcsh && \
#removed sudo
bash OS_notes.linux_ubuntu_20_64_a_admin.txt 2>&1 | tee o.ubuntu_20_a.txt && \
tcsh OS_notes.linux_ubuntu_20_64_b_user.tcsh 2>&1 | tee o.ubuntu_20_b.txt
#dcm2niix
RUN curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
#ANTsR, ANTsRCore, ITKR
RUN git clone https://github.com/stnava/ITKR.git && \
git clone https://github.com/ANTsX/ANTsRCore.git && \
git clone https://github.com/ANTsX/ANTsR.git && \
R -e 'install.packages(c("Rcpp", "RcppEigen", "magrittr"))' && \
R CMD INSTALL ITKR && \
R CMD INSTALL ANTsRCore && \
R CMD INSTALL ANTsR
#COPY the specified folder structure and associated scripts to /usr/local/tomcat
COPY ./aidp_docker/ /usr/local/tomcat
#COPY wAIDP.war to the image
COPY ./wAIDP.war /usr/local/tomcat/webapps
#build complete
RUN echo 'Build complete!'
#runs the Docker image
CMD ["catalina.sh", "run"]