如何在 docker 文件中包含 shell 脚本套件

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.