This page instructs how to install Open Babel software to Palmetto The code and the issue tracker can be found here

  1. Request an interactive session. For example:

    $ qsub -I -l select=1:ncpus=8:mem=24gb:interconnect=fdr,walltime=3:00:00
    
  2. Load the required modules

    $ module load cmake/3.6.1 gcc/4.8.1 
    
  3. Install Eigen (latest version 3.3.7)

    $ wget http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
    $ tar -xvf 3.3.7.tar.gz
    $ cd eigen-eigen-323c052e1731
    $ mkdir build
    $ cd build
    $ cmake -DCMAKE_INSTALL_PREFIX=$HOME/applications/ ..
    $ make install
    
  4. Install wxWidgets (latest version 3.1.2)

    $ wget https://github.com/wxWidgets/wxWidgets/releases/download/v3.1.2/wxWidgets-3.1.2.tar.bz2
    $ tar -xvf wxWidgets-3.1.2.tar.bz2
    $ cd wxWidgets-3.1.2
    $ configure --prefix=$HOME/applications
    $ make
    $ make install
    
  5. Download Open Babel from source. Here we download the latest version 2.4.1.

    Upload the package openbabel-2.4.1.tar.gz to your Palmetto storage

    Unpack the downloaded file and go into openbabel source folder

    $ tar -xvf openbabel-2.4.1.tar.gz
    $ cd openbabel-2.4.1
    $ mkdir build
    $ cd build
    $ cmake ../openbabel-2.4.1 -DCMAKE_INSTALL_PREFIX=$HOME/applications/ -DLIB_INSTALL_DIR=$HOME/applications/lib -DEIGEN3_INCLUDE_DIR=$HOME/applications/include/eigen3 -DBUILD_GUI=ON ..
    $ make -j4
    $ make test #make sure that all tests should be passed
    $ make install   
    
  6. The obabel executable file will be created in the installation folder: /home/username/applications/bin. Make sure you set the correct environment PATH in ~/.bashrc file

    export PATH=$PATH:$HOME/applications/bin