Singularity container

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I wrote the following singularity container



BootStrap: docker
From: debian:stretch-backports

%help
A container with 3d-dna

%post
apt-get update && apt-get -y upgrade
apt-get -y install
build-essential
wget
bzip2
ca-certificates
libglib2.0-0
libxext6
libsm6
libxrender1
git

rm -rf /var/lib/apt/lists/*
apt-get clean

# download and install Miniconda
echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
/bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda
rm -rf Miniconda2-latest-Linux-x86_64.sh

# add bioconda channels
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda update conda

# install 3d-dna dependecies
conda install lastz=1.0.4
conda install openjdk=8.0.152
conda install gawk=4.2.1
conda install coreutils=8.30
conda install parallel=20180522
conda install python=2.7
conda install numpy=1.15.1
conda install scipy=1.1.0
conda install matplotlib=2.2.3

# install 3d-dna
git clone https://github.com/theaidenlab/3d-dna.git

%environment
PATH=/opt/conda/bin:$PATH


Could anyone please show me how to build and access the scripts inside the 3d-dna folder?










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    up vote
    0
    down vote

    favorite












    I wrote the following singularity container



    BootStrap: docker
    From: debian:stretch-backports

    %help
    A container with 3d-dna

    %post
    apt-get update && apt-get -y upgrade
    apt-get -y install
    build-essential
    wget
    bzip2
    ca-certificates
    libglib2.0-0
    libxext6
    libsm6
    libxrender1
    git

    rm -rf /var/lib/apt/lists/*
    apt-get clean

    # download and install Miniconda
    echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
    wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
    /bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda
    rm -rf Miniconda2-latest-Linux-x86_64.sh

    # add bioconda channels
    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda update conda

    # install 3d-dna dependecies
    conda install lastz=1.0.4
    conda install openjdk=8.0.152
    conda install gawk=4.2.1
    conda install coreutils=8.30
    conda install parallel=20180522
    conda install python=2.7
    conda install numpy=1.15.1
    conda install scipy=1.1.0
    conda install matplotlib=2.2.3

    # install 3d-dna
    git clone https://github.com/theaidenlab/3d-dna.git

    %environment
    PATH=/opt/conda/bin:$PATH


    Could anyone please show me how to build and access the scripts inside the 3d-dna folder?










    share|improve this question

























      up vote
      0
      down vote

      favorite









      up vote
      0
      down vote

      favorite











      I wrote the following singularity container



      BootStrap: docker
      From: debian:stretch-backports

      %help
      A container with 3d-dna

      %post
      apt-get update && apt-get -y upgrade
      apt-get -y install
      build-essential
      wget
      bzip2
      ca-certificates
      libglib2.0-0
      libxext6
      libsm6
      libxrender1
      git

      rm -rf /var/lib/apt/lists/*
      apt-get clean

      # download and install Miniconda
      echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
      wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
      /bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda
      rm -rf Miniconda2-latest-Linux-x86_64.sh

      # add bioconda channels
      conda config --add channels defaults
      conda config --add channels conda-forge
      conda config --add channels bioconda
      conda update conda

      # install 3d-dna dependecies
      conda install lastz=1.0.4
      conda install openjdk=8.0.152
      conda install gawk=4.2.1
      conda install coreutils=8.30
      conda install parallel=20180522
      conda install python=2.7
      conda install numpy=1.15.1
      conda install scipy=1.1.0
      conda install matplotlib=2.2.3

      # install 3d-dna
      git clone https://github.com/theaidenlab/3d-dna.git

      %environment
      PATH=/opt/conda/bin:$PATH


      Could anyone please show me how to build and access the scripts inside the 3d-dna folder?










      share|improve this question















      I wrote the following singularity container



      BootStrap: docker
      From: debian:stretch-backports

      %help
      A container with 3d-dna

      %post
      apt-get update && apt-get -y upgrade
      apt-get -y install
      build-essential
      wget
      bzip2
      ca-certificates
      libglib2.0-0
      libxext6
      libsm6
      libxrender1
      git

      rm -rf /var/lib/apt/lists/*
      apt-get clean

      # download and install Miniconda
      echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
      wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
      /bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda
      rm -rf Miniconda2-latest-Linux-x86_64.sh

      # add bioconda channels
      conda config --add channels defaults
      conda config --add channels conda-forge
      conda config --add channels bioconda
      conda update conda

      # install 3d-dna dependecies
      conda install lastz=1.0.4
      conda install openjdk=8.0.152
      conda install gawk=4.2.1
      conda install coreutils=8.30
      conda install parallel=20180522
      conda install python=2.7
      conda install numpy=1.15.1
      conda install scipy=1.1.0
      conda install matplotlib=2.2.3

      # install 3d-dna
      git clone https://github.com/theaidenlab/3d-dna.git

      %environment
      PATH=/opt/conda/bin:$PATH


      Could anyone please show me how to build and access the scripts inside the 3d-dna folder?







      container






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      edited Sep 17 at 1:46









      Rui F Ribeiro

      36.8k1273117




      36.8k1273117










      asked Sep 17 at 1:46









      user3523406

      477




      477

























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