pnlpipe_software submodule

This module is used as a submodule to install required software for pnlpipe and pnlNipype installation.

Defining PYTHONPATH like below enables from pnlpipe_software import * inside the software installation scripts.

export PYTHONPATH=/abs/directory/of/pnlpipe_software/

The python scripts in this module download and install software. They are essentially wrapper around git, cmake, and make commands.

If you would like to use this submodule separately from pnlpipe or pnlNipype, you should clone the submodule https://github.com/pnlbwh/cmd.git and use cmd/install.py script.

git clone https://github.com/pnlbwh/cmd.git
git clone https://github.com/pnlbwh/pnlpipe_software.git

Then upon defining PYTHONPATH and PNLPIPE_SOFT, you can install software as follows:

export PYTHONPATH=/abs/directory/of/pnlpipe_software/
export PNLPIPE_SOFT=/directory/for/software/    # this is where software modules are installed

cmd/install.py -h                               # see usage
cmd/install.py UKFTractography                  # install default branch
cmd/install.py -v master dcm2niix               # install master branch
cmd/install.py ANTs -v 6f403d7                  # install release/branch defined by hash

NOTE Support for the following scripts are deprecated because they are not used with pnlpipe/pnlNipye anymore:

• FreeSurfer.py
• HCPPipelines.py
• Slicer.py
• mrtrix3.py
• nrrdchecker.py
• whitematteranalysis.py