command not found inside Docker

entrypoint.sh

#!/bin/bash

# Add local user
# Either use the LOCAL_USER_ID if passed in at runtime or
# fallback

USER_ID=${LOCAL_USER_ID:-9001}

echo "Starting with UID : $USER_ID"
useradd --shell /bin/bash -u $USER_ID -o -c "" -m user
export HOME=/home/user

exec /usr/local/bin/gosu user "$@"

Howto

# Howto

cd samtools
docker build -t samtools .
cd ../samtools-run
docker build -t samtools-run .

docker run -it -e LOCAL_USER_ID=`id -u $USER`  samtools-run

user@d2a1d8faa190:/usr/local/samtools-0.1.19$ samtools
bash: samtools: command not found

samtools - Dockerfile

FROM ubuntu:16.04

# Setup OS
RUN apt-get update -y && apt-get upgrade -y
#RUN apt-get -y install python-software-properties
RUN apt-get -y install software-properties-common
#RUN add-apt-repository ppa:nebc/bio-linux 
#RUN add-apt-repository ppa:openjdk-r/ppa 
RUN apt-get update -y 

RUN apt-get install -y wget curl unzip git parallel openjdk-8-jre python-pip python-dev build-essential gfortran zlib1g-dev 
 
# Define commonly used JAVA_HOME variable
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64	

# Bowtie (https://sourceforge.net/projects/bowtie-bio)
ENV BOWTIE_VAR 1.1.2
COPY bowtie-${BOWTIE_VAR}-linux-x86_64.zip /tmp/
RUN unzip /tmp/bowtie-${BOWTIE_VAR}-linux-x86_64.zip -d /usr/local/ && \
    rm /tmp/bowtie-${BOWTIE_VAR}-linux-x86_64.zip && \
    find /usr/local/bowtie-${BOWTIE_VAR} -type f -executable -exec ln -s {} /usr/local/bin \; && \
    find /usr/local/bowtie-${BOWTIE_VAR}/scripts -type f -executable -exec ln -s {} /usr/local/bin \;

# Samtools
ENV SAMTOOLS_VER 0.1.19
ADD samtools-${SAMTOOLS_VER}.tar.bz2 /usr/local/
RUN apt-get install libncurses5-dev -y
WORKDIR /usr/local/samtools-${SAMTOOLS_VER}
RUN make 
RUN chown -R 1000 /usr/local/samtools-${SAMTOOLS_VER}
RUN chmod -R a+rX /usr/local/samtools-${SAMTOOLS_VER}
RUN find /usr/local/samtools-${SAMTOOLS_VER} -type f -executable -exec ln -s {} /usr/local/bin \; && \
    find /usr/local/samtools-${SAMTOOLS_VER}/misc -type f -executable -exec ln -s {} /usr/local/bin \; && \
    find /usr/local/samtools-${SAMTOOLS_VER}/bcftools -type f -executable -exec ln -s {} /usr/local/bin \;

# Created files have not root owner (https://denibertovic.com/posts/handling-permissions-with-docker-volumes/)
VOLUME ["/export/", "/data/", "/var/lib/docker"]
RUN apt-get update && apt-get -y --no-install-recommends install \
    ca-certificates \
    curl

RUN gpg --keyserver ha.pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4
RUN curl -o /usr/local/bin/gosu -SL "https://github.com/tianon/gosu/releases/download/1.4/gosu-$(dpkg --print-architecture)" \
    && curl -o /usr/local/bin/gosu.asc -SL "https://github.com/tianon/gosu/releases/download/1.4/gosu-$(dpkg --print-architecture).asc" \
    && gpg --verify /usr/local/bin/gosu.asc \
    && rm /usr/local/bin/gosu.asc \
    && chmod +x /usr/local/bin/gosu

COPY entrypoint.sh /usr/local/bin/entrypoint.sh
RUN chmod +x /usr/local/bin/entrypoint.sh
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]


#USER ubuntu



# Mark folders as imported from the host.
# VOLUME ["/export/", "/data/", "/var/lib/docker"]

#ENTRYPOINT ["python3", "/BUSCO_v1.1b1/BUSCO_v1.1b1.py"]
#ENTRYPOINT ["/bin/bash"]

# Cleanup
#RUN DEBIAN_FRONTEND=noninteractive apt-get purge -y build-essential
#RUN DEBIAN_FRONTEND=noninteractive apt-get purge -y gfortran
#RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Include all needed scripts and libraries from the host
# compressed archives will be extracted automatically
# ADD ./snakefile /galaxy-central/
# Execute the pipeline

samtools-run - Dockerfile

FROM samtools

CMD ["/bin/bash"]