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qunex / Overview / Installation

Installing from source and dependencies

Installation of source code

Step 1: Clone all QuNex repositories and initiate submodules:

  • Clone: git clone git@bitbucket.org:oriadev/qunex.git
  • Initiate submodules from inside cloned repository folder: git submodule init
  • Pull and update all submodules: git pull --recurse-submodules && git submodule update --recursive
  • Update submodules to the latest commit on origin: git submodule foreach git pull origin master
  • Switch all submodules to the master branch: git submodule foreach git checkout master

Step 2: Configure your OS environment. Set the environmental variables TOOLS and QUNEXREPO. For example, if QuNex is located at /qunex_suite/qunex, set TOOLS=/qunex_suite/ and QUNEXREPO=qunex. The easiest way to do this is by adding the following lines to your .bash_profile:

TOOLS=<path to the root of where the software is installed>
QUNEXREPO=<relative path to the QuNex folder within $TOOLS, e.g. 'qunex'>
export TOOLS QUNEXREPO

Step 3: Install all necessary external dependencies:

Step 4: Source the Qunex environment. The most convenient way is to make the OS automatically source it by adding the following line to .bash_profile:

source $TOOLS/$QUNEXREPO/env/qunex_environment.sh

Step 5: Setup the external dependencies. External tools should be installed inside the $TOOLS folder:

  • The qunex_environment.sh script automatically sets assumptions for dependency paths. These can be changed by the user.
  • For more info on how to define specific QuNex dependencies paths run: qunex --envsetup.

Updating the QuNex Suite from Source

  • To update the main QuNex repository and all the submodules run:
git pull
git submodule update --recursive --remote
  • For this to work you need to have an active git account and read access to the main QuNex repository and all submodules.

QuNex environment setup

All the listed packages have to be either available on the system level or installed in the TOOLS directory. Please review and edit $TOOLS/$QUNEXREPO/env/qunex_environment.sh to ensure that all the dependencies are configured correctly. Once configured, for a full report of the QuNex Suite installed environment the user can run the following from the command line:

qunex_environment_status

The default locations expected by $TOOLS/$QUNEXREPO/env/qunex_environment.sh are listed below. A user can always change these manually after the environment script is run.

  TOOLS                               --> The base folder for the dependency installation
  │ 
  ├── qunex                           --> Env. Variable => QUNEXREPO -- All QuNex Suite repositories (https://bitbucket.org/oriadev/qunex)
  │ 
  ├── env                             --> conda environments with python packages
  │   └── qunex                       --> Env. Variable => QUNEXENV (python2.7 versions of the required packages)
  │
  ├── HCP                             --> Human Connectome Pipelines Folder (https://github.com/Washington-University/HCPpipelines)
  │   ├── HCPpipelines                --> Env. Variable => HCPPIPEDIR
  │   └── hcp-asl                     --> HCP ASL pipelines
  │
  ├── dcm2niix                        --> dcm2niix conversion tool (https://github.com/rordenlab/dcm2niix)
  │   └── dcm2niix.                   --> Env. Variable => DCMNIIDIR
  │
  ├── dicm2nii                        --> dicm2nii conversion tool (https://github.com/xiangruili/dicm2nii)
  │   └── dicm2nii.                   --> Env. Variable => DICMNIIDIR
  │
  ├── freesurfer                      --> FreeSurfer (http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-HCP/)
  │   └── freesurfer-<VERSION>        --> Env. Variable => FREESURFER_HOME (v6.0 or later stable for all other data)
  │
  ├── fsl                             --> FSL (v6.0.3 or above with GPU-enabled DWI tools; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)
  │   ├── fsl-<VERSION>               --> FSL installation
  │   ├── fsl                         --> Link to FSL installation, env. Variable => FSLDIR
  │   └── fix.                        --> Env. Variable => FSL_FIXDIR (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide)
  │
  ├── matlab                          --> MATLAB vR2017b or higher. If MATLAB is installed system-wide then a symlink is created here.
  │   ├── matlab-latest               --> Env. Variable => MATLABDIR
  │   └── matlab-latest/bin           --> Env. Variable => MATLABBINDIR
  │
  ├── miniconda                       --> Env. Variable => CONDADIR, miniconda2 for python environment management (https://conda.io/projects/conda/en/latest/user-guide/install/)
  │
  ├── octave                          --> Octave v.4.4.1 or higher. If Octave is installed system-wide then a symlink is created here
  │   ├── octave-<VERSION>            --> Octave installation
  │   ├── octave                      --> Env. Variable => OCTAVEDIR, link to Octave installation
  │   ├── octave/bin                  --> Env. Variable => OCTAVEBINDIR
  │   └── octavepkg                   --> Env. Variable => OCTAVEPKGDIR -- If Octave packages need manual deployment then the installed packages go here.
  │
  ├── palm                            --> PALM: Permutation Analysis of Linear Models (https://github.com/andersonwinkler/PALM)
  │   ├── palm-o                      --> Env. Variable => PALMDIR (If using Octave)
  │   └── palm-m                      --> Env. Variable => PALMDIR (If using MATLAB)
  │
  ├── R                               --> R Statistical computing environment
  │   └── R-<VERSION>                 --> Env. Variable => RDIR
  │
  ├── gradunwarp                      --> HCP version of gradunwarp (https://github.com/Washington-University/gradunwarp)
  │   ├── gradunwarp-<VERSION>        --> Gradunwarp installation
  │   └── gradunwarp                  --> Env. Variable => GRADUNWARPDIR, link to granduwarp installation
  │
  └── workbench/workbench-<VERSION>   --> Connectome Workbench (v1.0 or above; https://www.humanconnectome.org/software/connectome-workbench)
      └── workbench-<VERSION>         --> Workbench installation
      └── workbench                   --> Env. Variable = HCPWBDIR, link to Workbench installation

These defaults can be redefined if the above paths are declared as global variables in the .bash_profile profile after loading the QuNex environment.

Additional installation notes

For the tools that require compilation and/or installation, make sure that you download them to the temporary folder and then install them in the correct location. E.g. gradunwarp would be installed by:

cd $TMP
git clone https://github.com/Washington-University/gradunwarp.git
cd gradunwarp
python setup.py install --prefix=$TOOLS/pylib/gradunwarp

Instructions for installation of QuNex and external dependencies

Updated