CLI Usage

This section describes how to run a workflow created in GUI on a cluster or in Command Line Interface (CLI), such as Terminal.

CLI execution

1. Config File Settings

Config files can be downloaded from Record on the GUI. Config files may be edited, such as duplicating and changing parameters. Place the config file required by Snakemake in the desired location for running with the CLI.

2. Set Environment Variables for Save Paths

Change environment variables. Change the environment variable as follows, because the default setting refers to the directory under /tmp/studio.

export OPTINIST_DIR="your_saving_dir"

With environment variables set, input refers to {OPTINIST_DIR}/input/ and results are output to {OPTINIST_DIR}/output.

3. Input File Settings

Input files are stored under /{OPTINIST_DIR}/input/. For example, if there is mouse_123.tiff, it is stored as /{OPTINIST_DIR}/input/mouse_123.tiff.

4. Execution

It can be executed in the CLI by running run_cluster.py.

The parameter arguments are as follows.

config [string, required]: Path of config.yaml file set in step 1
cores [int, optional, default: 2]: Specifies the number of CPU cores.
forceall [bool, optional, default: false]: Whether to overwrite existing results or not.
use_conda [bool, optional, default: true]: Whether to use the conda virtual environment or not. If not, it is necessary to have caiman, suite2p, etc. installed in the execution environment.

The command executes the following

python run_cluster.py --config="{snakemake.yaml file path}"

5.Output Result

The results are stored in {OPTINIST_DIR}/output/{unique_id}. If you want to visualize the results, you can move this directory to local, and you can check the results in GUI.