xrobin/singularity-pymol-openbabel:latest

$ singularity pull shub://xrobin/singularity-pymol-openbabel:latest

Singularity Recipe

BootStrap: docker
From: centos:7

%runscript

   #"I can put here whatever I want to happen by default when the user runs the container"
   cat << EOF
This container includes the following apps:
PyMOL 2.0.7 - https://pymol.org
OpenBabel 2.4.1 - http://openbabel.org
To list them do "singularity apps pymol-openbabel.img"
EOF

%post
    # install some system deps
    #apt-get -y update
    #apt-get -y install locales curl bzip2
    #locale-gen en_US.UTF-8
    #apt-get clean
    yum install -y curl bzip2
    # System dependencies for PyMOL
    yum install -y libGL libGLU qt5-qtbase-gui

    # Openbabel from the system?
    # yum install openbabel

    # download and install miniconda2
    if [ ! -x "/opt/miniconda2/bin/conda" ]; then
      curl -sSL -O https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
      bash Miniconda2-latest-Linux-x86_64.sh -p /opt/miniconda2 -b
      rm -fr Miniconda2-latest-Linux-x86_64.sh
    fi

    # use conda to install some bioinfo tools
    export PATH=/opt/miniconda2/bin:$PATH
    conda install --yes -c bioconda openbabel
    conda install --yes -c schrodinger pymol 

%environment
    export LANG=en_US.UTF-8
    export LANGUAGE=en_US:en
    export LC_ALL=en_US.UTF-8
    export PATH=/opt/miniconda2/bin:$PATH

%apphelp PyMOL
    "PyMOL version 2.0.7"

%apprun PyMOL
    /opt/miniconda2/bin/pymol

%apphelp OpenBabel
    "OpenBabel version 2.4.1"

%apprun OpenBabel
    /opt/miniconda2/bin/obabel

Collection

• Name: xrobin/singularity-pymol-openbabel
• License: None

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