cli¶

Much of the interaction a user will want to do with gsmodutils will be through the command line tools. This section gives a brief overview of these tools, with simple examples that should be applicable to most users.

gsmodutils¶

Command line tools for management of gsmodutils genome scale model projects

gsmodutils [OPTIONS] COMMAND [ARGS]...

addmodel¶

Add a model to a specified gsm project. If validation is selected, where the model fails to conform to cobra standards, the model will not be added to the project.

gsmodutils addmodel [OPTIONS] PATH

Options

--project_path <project_path>¶: gsmodutils project path

--validate, --no-validate¶: Chose to validate the model before it is added.

Arguments

PATH¶: Required argument

diff¶

View the changed reactions between a model and a base model

gsmodutils diff [OPTIONS] MODEL_PATH

Options

--base_model <base_model>¶: Project model to compare with

--project_path <project_path>¶: gsmodutils project path

--parent <parent>¶: A parent design

--output <output>¶: A location to output the diff as a sjon file

--names, --no-names¶: Output names of added or changed metabolites and reactions

Arguments

MODEL_PATH¶: Required argument

dimport¶

Import a design into a model. This can be new or overwrite an existing design.

gsmodutils dimport [OPTIONS] MODEL_PATH IDENTIFIER

Options

--name <name>¶: Formal design name (longer than identifier)

--description <description>¶: Description of what the design does

--project_path <project_path>¶: gsmodutils project path

--parent <parent>¶: A parent design that was applied first to avoid replication.

--base_model <base_model>¶: Model that design is based on

--overwrite, --no-overwrite¶: overwrite existing design

--from_diff, --not_from_diff¶: load a diff file instead of compatible model

Arguments

MODEL_PATH¶: Required argument

IDENTIFIER¶: Required argument

docker¶

Create a dockerfile for the project

gsmodutils docker [OPTIONS]

Options

--project_path <project_path>¶: gsmodutils project path

--overwrite, --no-overwrite¶: overwrite existing dockerfile

--build, --no-build¶: build docker container

--save, --no-save¶: save docker image of tagged container

--tag <tag>¶: tag name for docker container (appended to project name).

--save_path <save_path>¶: Save path for shared docker image

export¶

Export a given model with a specific design and conditions applied

gsmodutils export [OPTIONS] [json|yaml|sbml|matlab|mat|m|scrumpy|spy] FILEPATH

Options

--project_path <project_path>¶: gsmodutils project path

--model_id <model_id>¶: model id

--conditions <conditions>¶: conditions to apply

--design <design>¶: design to apply

--overwrite, --no-overwrite¶: model id

Arguments

FILE_FORMAT¶: Required argument

FILEPATH¶: Required argument

iconditions¶

Add a given set of media condtions from a model (this ignores any added or removed reactions or metabolites)

gsmodutils iconditions [OPTIONS] PATH IDENT

Options

--project_path <project_path>¶: gsmodutils project path

--apply_to <apply_to>¶: Description of what the design does

--growth, --no_growth¶: Should these conditions allow growth or not

Arguments

PATH¶: Required argument

IDENT¶: Required argument

info¶

Display all the information about a gsmodutils project (list models, paths, designs etc.

gsmodutils info [OPTIONS]

Options

--project_path <project_path>¶: gsmodutils project path

init¶

Create a new gsmodutils project

gsmodutils init [OPTIONS] PROJECT_PATH DEFAULT_MODEL_PATH

Options

--name <name>¶

--description <description>¶: Project description

--author <author>¶: Project name

--email <email>¶: Author email

--add_models <add_models>¶: paths to additional model files, separated by space

--validate, --skip_validation¶: Require the model to be validated

Arguments

PROJECT_PATH¶: Required argument

DEFAULT_MODEL_PATH¶: Required argument

test¶

Run tests for a project

gsmodutils test [OPTIONS]

Options

--project_path <project_path>¶: gsmodutils project path

--test_id <test_id>¶: specify a given test identifier to run - pyton filename, function orjson_filename entry. Individual tests separated by double colons -

--skip_default, --no_skip_default¶: skip default tests

--verbose, --no_verbose¶: Display succesfully run test assertions

--log_path <log_path>¶: path to output json test log