funcx-openfold

FuncX OpenFold interface.

Install

Please run the following commands to install:

git clone https://github.com/ramanathanlab/funcx-openfold.git
cd funcx-openfold
pip3 install -U pip setuptools wheel
pip3 install -r requirements/requirements.txt
pip3 install -e .

To test the installation and view the CLI command options:

funcx-openfold --help
funcx-openfold register --help
funcx-openfold run --help
funcx-openfold status --help

CLI

Usage:

$ funcx-openfold COMMAND [ARGS]...

Options:

• --install-completion: Install completion for the current shell.
• --show-completion: Show completion for the current shell, to copy it or customize the installation.
• --help: Show this message and exit.

Commands:

• register: Register funcX OpenFold function and output the --function UUID.
• run: Submit an OpenFold job to the cluster to fold --fasta with a registered --function UUID.
• status: Check the status of the a funcX task given the --task-id.

register

Register funcX OpenFold function and output the --function UUID.

Usage:

$ register [OPTIONS]

Options:

• --help: Show this message and exit.

run

Submit an OpenFold job to the cluster to fold --fasta using the registered --function UUID.

Usage:

$ run [OPTIONS]

Options:

• --endpoint UUID: UUID for cluster endpoint. [required]
• --function UUID: UUID for registered function. [required]
• -f, --fasta FILE: Fasta file containing sequence to fold. [required]
• -d, --database PATH: Path to batabase on cluster. [required]
• -o, --output PATH: Output directory on cluster. [required]
• --openfold PATH: Path to OpenFold repository on cluster. [required]
• --help: Show this message and exit.

status

Check the status of the a funcX task given the --task-id.

Usage:

$ status [OPTIONS] TASK_ID

Arguments:

• TASK_ID: A task UUID. [required]

Options:

• --help: Show this message and exit.

Contributing

To install:

pip3 install -U pip setuptools wheel
pip3 install -r requirements/dev.txt
pip3 install -r requirements/requirements.txt
pip3 install -e .

To generate the documentation: typer cli.py utils docs