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尝试为此包构建 Singularity 映像时： https ://bitbucket.org/MAVERICLab/vcontact2.git

我得到：

{cut}
I: Configuring login...
I: Configuring adduser...
I: Configuring apt...
I: Configuring util-linux...
I: Configuring mount...
I: Configuring sysvinit-utils...
I: Configuring libc-bin...
I: Unpacking the base system...
W: Failure while installing base packages.  This will be re-attempted up to five times.
W: See /usr/local/var/singularity/mnt/container/debootstrap/debootstrap.log for details

我有：

  • 奇点 2.5.2-dist
  • Ubuntu 16.04.6 LTS（我通过 apt-get 安装：dh-autoreconf、build-essential、libarchive-dev、debootstrap）

该错误对我来说看起来很模糊，看起来有些软件包无法下载。我应该怎么解决这个问题？（我不想使用新版本的 Singularity）

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1 回答 1

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如果您愿意修改定义文件并使用不同的引导源，则以下内容可以在 18.04 LTS 上成功构建，并且也应该在 16.04 上构建。

# Use docker instead of debootstrap, could also probably use a newer version if desired
BootStrap: docker
From: ubuntu:xenial

%environment
    # note: this only active in `singularity exec` and `singularity run` steps
    export PATH=/miniconda3/bin:$PATH

%runscript
    exec vcontact "$@"

%post
    apt-get update && apt-get install -y automake build-essential bzip2 wget git default-jre unzip

    export BINPATH=/usr/local/bin

    # Install miniconda to save dependency nightmares
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -b -f -p /miniconda3/
    rm Miniconda3-latest-Linux-x86_64.sh

    # pull the conda functions in
    . /miniconda3/etc/profile.d/conda.sh
    # make pip, etc. available while in %post
    export PATH="/miniconda3/bin:$PATH"

    conda install -y -c conda-forge hdf5 pytables pypandoc biopython networkx numpy pandas scipy scikit-learn psutil pip
    conda install -y -c bioconda mcl blast diamond

    pip install setuptools-markdown

    # Install vContact
    git clone https://bitbucket.org/MAVERICLab/vcontact2.git
    cd vcontact2 && pip install .

    # Bug with setuptools?
    cp /vcontact2/vcontact/data/ViralRefSeq-prokaryotes-v??.* /miniconda3/lib/python3.7/site-packages/vcontact/data/

    # 'Install' ClusterONE
    cd / && wget http://www.paccanarolab.org/static_content/clusterone/cluster_one-1.0.jar
    mv /cluster_one-1.0.jar $BINPATH && chmod +x $BINPATH/cluster_one-1.0.jar

    # Clean stuff up
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
    conda clean --yes --tarballs --packages --source-cache

    # TACC's Stampede compliant, for iVirus/CyVerse
    mkdir /home1 && mkdir /scratch && mkdir /work

我对我更改的行发表了评论，但如果这不是建立在您的系统上或对更改有疑问，请告诉我。

于 2019-07-11T12:28:52.423 回答