README.rst

C-PAC Python Package

A Python package that wraps C-PAC, enabling users to install cpac with pip and run from the command line.

Description

C-PAC Python Package is a lightweight Python package that handles interfacing a user's machine and a C-PAC container through a command line interface.

Dependencies

• Python ≥3.6
• pip
• At least one of:
  • Docker
  • Singularity ≥2.5&≤3.0

Usage

cpac --help
usage: cpac [-h] [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
            [--version] [-v] [-vv] [--working_dir PATH] [--temp_dir PATH]
            [--output_dir PATH] [-o OPT [OPT ...]]
            [-B CUSTOM_BINDING [CUSTOM_BINDING ...]]
            {run,group,utils,crash} ...

cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io>
containerized images. If no platform nor image is specified, cpac will try
Docker first, then try Singularity if Docker fails.

positional arguments:
  {run,group,utils,crash}

optional arguments:
  -h, --help            show this help message and exit
  --platform {docker,singularity}
  --image IMAGE         path to Singularity image file OR name of Docker image
                        (eg, "fcpindi/c-pac"). Will attempt to pull from
                        Singularity Hub or Docker Hub if not provided.
  --tag TAG             tag of the Docker image to use (eg, "latest" or
                        "nightly").
  --version             show program's version number and exit
  -v, --verbose         set loglevel to INFO
  -vv, --very-verbose   set loglevel to DEBUG
  --working_dir PATH    working directory
  --temp_dir PATH       directory for temporary files
  --output_dir PATH     directory where output files should be stored
  -o OPT [OPT ...], --container_option OPT [OPT ...]
                        parameters and flags to pass through to Docker or
                        Singularity
  -B CUSTOM_BINDING [CUSTOM_BINDING ...], --custom_binding CUSTOM_BINDING [CUSTOM_BINDING ...]
                        directory to bind to container with a different path
                        than the real path in the format
                        real_path:container_path (eg,
                        /home/C-PAC/run5/outputs:/outputs). Use absolute paths
                        for both paths