adamewing/bamsurgeon

Dockerfile doesn't build

cfriedline opened this issue · 3 comments

cfriedline commented

Hi there. Thanks for all of the great work on this. The Dockerfile is not building, however.

Getting this error:

E: The repository 'http://security.ubuntu.com/ubuntu disco-security Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu disco Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu disco-updates Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu disco-backports Release' does not have a Release file.

The full log is below:

Sending build context to Docker daemon    447MB
Step 1/15 : FROM ubuntu:19.04
19.04: Pulling from library/ubuntu
4dc9c2fff018: Pull complete
0a4ccbb24215: Pull complete
c0f243bc6706: Pull complete
5ff1eaecba77: Pull complete
Digest: sha256:2adeae829bf27a3399a0e7db8ae38d5adb89bcaf1bbef378240bc0e6724e8344
Status: Downloaded newer image for ubuntu:19.04
 ---> c88ac1f841b7
Step 2/15 : MAINTAINER Adam Ewing <adam.ewing@gmail.com>
 ---> Running in ddd6a624c0bf
Removing intermediate container ddd6a624c0bf
 ---> df1803705b4f
Step 3/15 : ENV PATH=$PATH:$HOME/bin
 ---> Running in c31879c3befb
Removing intermediate container c31879c3befb
 ---> cb800e6518d6
Step 4/15 : WORKDIR ~/
 ---> Running in 42a98a29bacc
Removing intermediate container 42a98a29bacc
 ---> cb3d7eb2757e
Step 5/15 : RUN apt-get update && apt-get install -y --no-install-recommends     python3     python3-dev     python3-numpy     python3-scipy     python3-pip     python3-setuptools     python3-wheel     zlib1g-dev     libbz2-dev     git     wget     libncurses5-dev     liblzma-dev     pkg-config     automake     autoconf     gcc     libglib2.0-dev     default-jre     samtools     bcftools     bwa     && rm -rf /var/lib/apt/lists/*
 ---> Running in ecd53994b0c0
Ign:1 http://archive.ubuntu.com/ubuntu disco InRelease
Ign:2 http://security.ubuntu.com/ubuntu disco-security InRelease
Ign:3 http://archive.ubuntu.com/ubuntu disco-updates InRelease
Err:4 http://security.ubuntu.com/ubuntu disco-security Release
  404  Not Found [IP: 91.189.88.142 80]
Ign:5 http://archive.ubuntu.com/ubuntu disco-backports InRelease
Err:6 http://archive.ubuntu.com/ubuntu disco Release
  404  Not Found [IP: 91.189.88.152 80]
Err:7 http://archive.ubuntu.com/ubuntu disco-updates Release
  404  Not Found [IP: 91.189.88.152 80]
Err:8 http://archive.ubuntu.com/ubuntu disco-backports Release
  404  Not Found [IP: 91.189.88.152 80]
Reading package lists...
E: The repository 'http://security.ubuntu.com/ubuntu disco-security Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu disco Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu disco-updates Release' does not have a Release file.
E: The repository 'http://archive.ubuntu.com/ubuntu disco-backports Release' does not have a Release file.
The command '/bin/sh -c apt-get update && apt-get install -y --no-install-recommends     python3     python3-dev     python3-numpy     python3-scipy     python3-pip     python3-setuptools     python3-wheel     zlib1g-dev     libbz2-dev     git     wget     libncurses5-dev     liblzma-dev     pkg-config     automake     autoconf     gcc     libglib2.0-dev     default-jre     samtools     bcftools     bwa     && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100
adamewing commented

Apologies for the delay. This appears to be a problem with connecting to the ubuntu repo, is this still an issue?

anderdnavarro commented

Yes, I just tried it and I had the same problem.

keithcallenberg commented

I changed to 20.04, then had to add make and switch from pip to pip3, but image now builds well for me:

FROM ubuntu:20.04
MAINTAINER Adam Ewing <adam.ewing@gmail.com>

ENV PATH=$PATH:$HOME/bin

WORKDIR ~/

#install the bareminimum and remove the cache
RUN apt-get update && apt-get install -y --no-install-recommends \
    python3 \
    python3-dev \
    python3-numpy \
    python3-scipy \
    python3-pip \
    python3-setuptools \
    python3-wheel \
    zlib1g-dev \
    libbz2-dev \
    git \
    wget \
    libncurses5-dev \
    liblzma-dev \
    pkg-config \
    automake \
    make \
    autoconf \
    gcc \
    libglib2.0-dev \
    default-jre \
    samtools \
    bcftools \
    bwa \
    && rm -rf /var/lib/apt/lists/*


RUN mkdir $HOME/bin

RUN wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz && tar -xvzf velvet_1.2.10.tgz
RUN make -C velvet_1.2.10
RUN cp velvet_1.2.10/velvetg $HOME/bin && cp velvet_1.2.10/velveth $HOME/bin

RUN git clone https://github.com/adamewing/exonerate.git
RUN cd exonerate && autoreconf -fi  && ./configure && make && make install

RUN pip3 install cython && pip3 install pysam

RUN git clone https://github.com/adamewing/bamsurgeon.git
RUN export PATH=$PATH:$HOME/bin && cd bamsurgeon && python3 setup.py install

CMD []
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