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
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