docker building failed using build.sh command

[joshuabhk]

Hi I have failed docker building process.

Step 11/35 : RUN cd /tmp && wget https://kent.dl.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz && tar xvfz vcftools_0.1.13.tar.gz && cd vcftools_0.1.13/ && make && sudo cp -r /tmp/vcftools_0.1.13/bin/* /usr/local/bin && sudo cp -r /tmp/vcftools_0.1.13/lib/perl5/site_perl/* /usr/local/lib && rm -rf /tmp/*
---> Running in c55c2f0cbc20
--2020-01-07 16:56:36-- https://kent.dl.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz
Resolving kent.dl.sourceforge.net (kent.dl.sourceforge.net)... 212.219.56.185
Connecting to kent.dl.sourceforge.net (kent.dl.sourceforge.net)|212.219.56.185|:443... connected.
ERROR: cannot verify kent.dl.sourceforge.net's certificate, issued by 'CN=Let's Encrypt Authority X3,O=Let's Encrypt,C=US':
Issued certificate has expired.
To connect to kent.dl.sourceforge.net insecurely, use `--no-check-certificate'.
The command '/bin/sh -c cd /tmp && wget https://kent.dl.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz && tar xvfz vcftools_0.1.13.tar.gz && cd vcftools_0.1.13/ && make && sudo cp -r /tmp/vcftools_0.1.13/bin/* /usr/local/bin && sudo cp -r /tmp/vcftools_0.1.13/lib/perl5/site_perl/* /usr/local/lib && rm -rf /tmp/*' returned a non-zero code: 5

My docker version is
Docker version 19.03.2, build 6a30dfca03

Thank you so much!

Josh

[julia326]

Hi Josh, sorry for the delayed reply - I'm looking into this issue, it looks like the VCFtools link is outdated in my Docker image so I'm updating this and a few other links.

In the meantime, if you want to use an existing Docker image for this pipeline rather than building it from scratch, you can grab it from DockerHub:

docker pull openvax/neoantigen-vaccine-pipeline:latest

[doctorchenzx]

Hi, I've resolved this problem by change the download link

# Install the Perl vcftools
RUN cd /tmp && wget https://sourceforge.net/projects/vcftools/files/vcftools_0.1.13.tar.gz && \
    tar xvfz vcftools_0.1.13.tar.gz && cd vcftools_0.1.13/ && make && \
    sudo cp -r /tmp/vcftools_0.1.13/bin/* /usr/local/bin && \
    sudo cp -r /tmp/vcftools_0.1.13/lib/perl5/site_perl/* /usr/local/lib && \
    rm -rf /tmp/*

ENV PERL5LIB /usr/local/lib

# Install Strelka
RUN mkdir $HOME/strelka && \
    cd /tmp && wget https://github.com/openvax/neoantigen-vaccine-pipeline/releases/download/0.3.0/strelka_workflow-1.0.14.tar.gz && \
    tar xvfz strelka_workflow-1.0.14.tar.gz && \
    cd strelka_workflow-1.0.14 && \
    ./configure prefix=$HOME/strelka && \
    make && \
    chmod -R a+rx ./* && \
    make install && \
    rm -rf /tmp/*

ENV STRELKA_BIN $HOME/strelka/bin

hope this work with you.