# CLI, Environment ## `catalog` ``` usage: quilt3 catalog [-h] [--detailed-help] [--host HOST] [--port PORT] [--no-browser] [navigation_target] Run Quilt catalog locally positional arguments: navigation_target Which page in the local catalog to open. Leave blank to go to the catalog landing page, pass in an S3 url (e.g. 's3://bucket/myfile.txt') to go to file viewer, or pass in a package name in the form 'BUCKET:USER/PKG' to go to the package viewer. optional arguments: -h, --help show this help message and exit --detailed-help, --detailed_help Display detailed information about this command and then exit --host HOST Bind socket to this host --port PORT Bind to a socket with this port --no-browser Don't open catalog in a browser after startup ``` Run the Quilt catalog on your machine. Running `quilt3 catalog` launches a Python webserver on your local machine that serves a catalog web app and provides required backend services using temporary AWS credentials. Temporary credentials are derived from your default AWS credentials (or active `AWS_PROFILE`) using `boto3.sts.get_session_token`. For more details about configuring and using AWS credentials in `boto3`, see the AWS documentation: #### Previewing files in S3 The Quilt catalog allows users to preview files in S3 by downloading and processing/converting them inside the Python webserver running on local machine. Neither your AWS credentials nor data requested goes through any third-party cloud services aside of S3. ## `config` ``` usage: quilt3 config [-h] [--set KEY=VALUE [KEY=VALUE ...]] [catalog_url] Configure Quilt positional arguments: catalog_url URL of catalog to config with, or empty string to reset the config optional arguments: -h, --help show this help message and exit --set KEY=VALUE [KEY=VALUE ...] Set a number of key-value pairs for config_values(do not put spaces before or after the = sign). If a value contains spaces, you should define it with double quotes: foo="this is a sentence". Note that values are always treated as strings. ``` ## `config-default-remote-registry` ``` usage: quilt3 config-default-remote-registry [-h] default_remote_registry Configure default remote registry for Quilt positional arguments: default_remote_registry The default remote registry to use, e.g. s3://quilt-ml optional arguments: -h, --help show this help message and exit ``` ## `disable-telemetry` ``` usage: quilt3 disable-telemetry [-h] Disable anonymous usage metrics optional arguments: -h, --help show this help message and exit ``` ## `install` ``` usage: quilt3 install [-h] [--registry REGISTRY] [--top-hash TOP_HASH] [--dest DEST] [--dest-registry DEST_REGISTRY] [--path PATH] name Install a package positional arguments: name Name of package, in the USER/PKG format optional arguments: -h, --help show this help message and exit --registry REGISTRY Registry where package is located, usually s3://MY- BUCKET. Defaults to the default remote registry. --top-hash TOP_HASH Hash of package to install. Defaults to latest. --dest DEST Local path to download files to. --dest-registry DEST_REGISTRY Registry to install package to. Defaults to local registry. --path PATH If specified, downloads only PATH or its children. ``` ## `list-packages` ``` usage: quilt3 list-packages [-h] registry List all packages in a registry positional arguments: registry Registry for packages, e.g. s3://quilt-example optional arguments: -h, --help show this help message and exit ``` ## `login` ``` usage: quilt3 login [-h] Log in to configured Quilt server optional arguments: -h, --help show this help message and exit ``` ## `logout` ``` usage: quilt3 logout [-h] Log out of current Quilt server optional arguments: -h, --help show this help message and exit ``` ## `push` ``` usage: quilt3 push --dir DIR [-h] [--registry REGISTRY] [--dest DEST] [--message MESSAGE] [--meta META] [--workflow WORKFLOW] [--force] [--dedupe] [--no-copy] name Pushes the new package to the remote registry positional arguments: name Name of package, in the USER/PKG format required arguments: --dir DIR Directory to add to the new package optional arguments: -h, --help show this help message and exit --registry REGISTRY Registry where to create the new package. Defaults to the default remote registry. --dest DEST Where to copy the objects in the package --message MESSAGE The commit message for the new package --meta META Sets package-level metadata. Format: A json string with keys in double quotes '{"key": "value"}' --workflow WORKFLOW Workflow ID or empty string to skip workflow validation. If not specified, the default workflow will be used. --force Skip the parent top hash check and create a new revision even if your local state is behind the remote registry. --dedupe Skip the push if the local package hash matches the remote hash. --no-copy Do not copy data. Package manifest entries will reference the data at the original location. ``` ## `verify` ``` usage: quilt3 verify [-h] --registry REGISTRY --top-hash TOP_HASH --dir DIR [--extra-files-ok] name Verify that package contents matches a given directory positional arguments: name Name of package, in the USER/PKG format optional arguments: -h, --help show this help message and exit --registry REGISTRY Registry where package is located, usually s3://MY- BUCKET --top-hash TOP_HASH Hash of package to verify --dir DIR Directory to verify --extra-files-ok Whether extra files in the directory should cause a failure ``` ## Environment variables ### `QUILT_DISABLE_CACHE` Turn off cache. Defaults to `False`. ```sh export QUILT_DISABLE_CACHE=true ``` ### `QUILT_DISABLE_USAGE_METRICS` Disable anonymous usage collection. Defaults to `False` ```sh export QUILT_DISABLE_USAGE_METRICS=true ``` ### `QUILT_MANIFEST_MAX_RECORD_SIZE` Maximum size of a record in package manifest. **Setting this variable is strongly discouraged.** Defaults to `1_000_000`. ### `QUILT_MINIMIZE_STDOUT` Turn off TQDM progress bars for log files. Defaults to `False` ```sh export QUILT_MINIMIZE_STDOUT=true ``` ### `QUILT_TRANSFER_MAX_CONCURRENCY` Number of threads for file transfers. Defaults to `10`. This variable could be tried for improving file transfer rate. The optimal value depends on network bandwidth, CPU performance, file sizes, etc. ```sh export QUILT_TRANSFER_MAX_CONCURRENCY=20 ``` ### `XDG_*` `quilt3` uses platformdirs so you can set one or more of the [XDG environment variables](https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html) to customize where `quilt3` writes to disk. For example, AWS Lambda requires the user to use `/tmp/*` as the scratch directory. You can override `quilt3.util.CACHE_PATH`, so that `quilt3 install` will succeed, by setting the `XDG_CACHE_HOME` environment variable in code or in your [AWS Lambda environment variables](https://docs.aws.amazon.com/lambda/latest/dg/configuration-envvars.html). > You must **set XDG environment variables before** `import quilt3` in order for them to take effect. ## Constants (see [util.py](https://github.com/quiltdata/quilt/blob/master/api/python/quilt3/util.py) for more) * `APP_AUTHOR` * `APP_NAME` * `BASE_DIR` - Base directory of the application * `BASE_PATH` - Base pathlib path for the application directory * `CACHE_PATH` - Pathlib path for the user cache directory * `CONFIG_PATH` - Base pathlib path for the application configuration file * `OPEN_DATA_URL` - Application data url * `PACKAGE_NAME_FORMAT` - Regex for legal package names * `TEMPFILE_DIR_PATH` - Base pathlib path for the application `tempfiles` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.quilt.bio/quilt-python-sdk/api-reference/cli.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.