How to include shell script suite in docker file - linux

Question

I am trying to create a docker image for BBMAP (https://sourceforge.net/projects/bbmap/files/latest/download) shell script suite available online along with samtools and picard.jar. I was able to run samtools and picard, but for some reason I am not able to add bbmap below. Can someone please let me know what I am missing here?
I am trying to add shell scripts to bin to run them as executables.
In my docker file below, this is where I need help:
&& wget -q https://sourceforge.net/projects/bbmap/files/latest/download \
&& tar -xjvf /tmp/download \
&& cp -av /tmp/bbmap/* /usr/bin/ \
Dockerfile:
FROM openjdk:8-jre
LABEL maintainer="AN <XXX#wustl.edu>"
LABEL org.label-schema.schema-version="1.0"
# LABEL org.label-schema.build-date=$BUILD_DATE
LABEL org.label-schema.name="an/samtofastq"
LABEL org.label-schema.description="Image for Reverting .bam"
ENV SAMTOOLS_VERSION 1.9
ENV PICARD_VERSION 2.20.8
WORKDIR /tmp
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
make \
gcc \
g++ \
libz-dev \
libbz2-dev \
liblzma-dev \
ncurses-dev \
bc \
libnss-sss \
time \
&& cd /tmp \
&& wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
&& tar xjvf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
&& cd /tmp/samtools-${SAMTOOLS_VERSION}/ \
&& make \
&& cp -av /tmp/samtools-${SAMTOOLS_VERSION}/samtools /usr/bin/ \
&& wget -q -O /usr/bin/picard.jar https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar \
&& wget -q https://sourceforge.net/projects/bbmap/files/latest/download \
&& tar -xjvf /tmp/download \
&& cp -av /tmp/bbmap/* /usr/bin/ \
&& ln -sf /usr/share/zoneinfo/America/Chicago /etc/localtime \
&& echo "America/Chicago" > /etc/timezone \
&& dpkg-reconfigure --frontend noninteractive tzdata \
&& apt-get clean all \
&& rm -rfv /var/lib/apt/lists/* /tmp/* /var/tmp/*
# COPY ./entrypoint.sh /usr/local/bin/
ENV PICARD /usr/bin/picard.jar
## Add ENV for Shell scripts from BBMAP
# ENV DEMUX /usr/bin/demuxbyname.sh
# ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
CMD ["/bin/bash"]
This is the error I am getting:
tar (child): /tmp/download: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now

Answer 1

Earlier in your script, you run:
cd /tmp/samtools-${SAMTOOLS_VERSION}/
So when you run this:
wget -q https://sourceforge.net/projects/bbmap/files/latest/download
The resulting file is:
/tmp/samtools-${SAMTOOLS_VERSION}/download
That means that when you run your tar command:
tar -xjvf /tmp/download
...it doesn't find the file because it isn't in /tmp.
Either change the path on the tar command, or add a cd /tmp to your script before downloading the file. Or pass something like -O /tmp/download.tar to your wget invocation.