Installation

Please note - if you’re a UNC-CH user, clpipe is already installed and accessible with the module system - please see the section below, “For UNC-CH Users”

Python Environment Setup

clpipe requires Python v3.7. If you have the priviledges to add python packages to your system, you can install the most recent version of clpipe with:

pip3 install --upgrade git+https://github.com/cohenlabUNC/clpipe.git

If you don’t have access to the global library (perhaps you are just a user of an HPC), you can install a local copy by adding the --user flag:

pip3 install --user --upgrade git+https://github.com/cohenlabUNC/clpipe.git

Pip will automatically install all required Python package dependencies.

External Dependencies

Singularity & Images

clpipe uses Singularity to run certain dependencies as images. clpipe has been tested against:

  • Singularity == v3.2.1

If you are a UNC-CH Longleaf user, Singularity is made available by default when launching jobs, so you do not need to explicitly add this dependency.

The following programs are required as images:

  • fMRIPrep >= v20

  • BIDS-validator >= v0.0.0

If you don’t already have a Singularity image of fMRIprep, head over to their site and follow the directions. You will have to change the fMRIprep image path in your configuration file.

Similarly, if you do not have a copy of the BIDS-validator Singularity image, you’ll need to obtain this image as well:

Other Dependencies

Additionally, clpipe requires the following tools to be installed in order to run its postprocessing and analysis steps (UNC-CH Users - this is handled by the clpipe module):

  • FSL >= v6.0.0

  • AFNI >= v20.0.00

  • R >= v4.0.0

For UNC-CH Users

If you are a Longleaf user and a member of the rc_hng_psx group, clpipe has already been installed for you via the module system.

clpipe is not currently available as part of Longleaf’s default module collection. Instead, it is provided through the HNG’s module directory, which you must setup manually.

First, make the HNG modules available:

module use /proj/hng/software/modules

Now save this module source to your default collection:

module save

You can then use the following to access the latest version of clpipe at any time:

module add clpipe

You also already have access to the latest singularity images for both fmriprep and the bids validator at /proj/hng/singularity_imgs, so there is no need to construct your own, unless you want a older version.

Batch Languages

clpipe was originally designed for use on the University of North Carolina at Chapel Hill’s HPC, Longleaf, which uses the SLURM task management system. The way clpipe handles what batch language to use is through a set of batch configuration files. These files are not directly exposed to users, and modification of these directly is ill advised. For other institutions that use task management systems other than SLURM, get in touch with the package maintainers, and we would be happy to help setup a configuration file for your system. In coming versions of clpipe, functionality will be added to allow users to change the batch management system settings.