C-PAC Python Package
Project description
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
At least one of:
Singularity ≥2.5&≤3.0
Usage
cpac --help
usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
[--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
[--working_dir PATH] [-v] [-vv]
{run,group,utils,pull,upgrade,crash} ...
cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images.
This commandline interface package is designed to minimize repetition.
As such, nearly all arguments are optional.
When launching a container, this package will try to bind any paths mentioned in
• the command
• the data configuration
An example minimal run command:
cpac run /path/to/data /path/for/outputs
An example run command with optional arguments:
cpac -B /path/to/data/configs:/configs \
--image fcpindi/c-pac --tag latest \
run /path/to/data /path/for/outputs \
--data_config_file /configs/data_config.yml \
--save_working_dir
Each command can take "--help" to provide additonal usage information, e.g.,
cpac run --help
positional arguments:
{run,group,utils,pull,upgrade,crash}
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
-o OPT, --container_option OPT
parameters and flags to pass through to Docker or Singularity
This flag can take multiple arguments so cannot be
the final argument before the command argument (i.e.,
run or any other command that does not start with - or --)
-B CUSTOM_BINDING, --custom_binding CUSTOM_BINDING
directories to bind with a different path in
the container than the real path of the directory.
One or more pairs in the format:
real_path:container_path
(eg, /home/C-PAC/run5/outputs:/outputs).
Use absolute paths for both paths.
This flag can take multiple arguments so cannot be
the final argument before the command argument (i.e.,
run or any other command that does not start with - or --)
--platform {docker,singularity}
If neither platform nor image is specified,
cpac will try Docker first, then try
Singularity if Docker fails.
--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.
If image is specified but platform is not, platform is
assumed to be Singularity if image is a path or
Docker if image is an image name.
--tag TAG tag of the Docker image to use (eg, "latest" or "nightly").
--working_dir PATH working directory
-v, --verbose set loglevel to INFO
-vv, --very-verbose set loglevel to DEBUG
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