> For the complete documentation index, see [llms.txt](https://docs.quilt.bio/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.quilt.bio/quilt-2-master/api/api-cli.md).

# Command line

## Core: build, push, and install packages

### `quilt build USER/PACKAGE PATH`

`PATH` may be a `build.yml` file or a directory. If a directory is given, Quilt will internally generate a build file (useful, e.g. for directories of images).

`build.yml` is for users who want fine-grained control over parsing.

### `quilt push USER/PACKAGE [--public ￨ --team]`

Stores the package in the registry |

### `quilt install USER/PACKAGE[/SUBPATH/...] [-x HASH ￨ -t TAG ￨ -v VERSION] [--force] [--meta-only]`

Installs a package or sub-package.

* `--force` - skips yes/no prompt in the case of overwrite
* `--meta-only` - install only the package metadata (useful for filtering large packages) 

### `quilt install @FILE=quilt.yml`

Installs all specified packages using the requirements syntax (above) |

### `quilt delete USER/PACKAGE`

Removes the package from the registry. Does not delete local data.

## Versioning

### `quilt log USER/PACKAGE`

Display push history

### `quilt version list USER/PACKAGE`

Display versions of a package

### `quilt version add USER/PACKAGE VERSION HASH`

Associate a version with a hash

### `quilt tag list USER/PACKAGE`

List available tags

### `quilt tag add USER/PACKAGE TAG HASH`

Associate a tag with a hash

### `quilt tag remove USER/PACKAGE TAG`

Remove a tag

## Access

### `quilt login [TEAM]`

Authenticate to a registry

### `quilt access list USER/PACKAGE`

List user who have access to a package |

### `quilt access add USER/PACKAGE USER_OR_GROUP`

Grant read access to a user or group (one of `public` or `team`)

### `quilt access remove USER_OR_GROUP`

Remove read access

## Local storage

### `quilt ls`

List installed packages

### `quilt rm USER/PACKAGE`

Remove a package from local storage (but not from the registry)

## Registry search

`quilt search "SEARCH STRING"` Search registry for packages by user or package name

## Export a package or subpackage

### `quilt export USER/PACKAGE`

Export data to current dir

### `quilt export USER/PACKAGE DEST`

Export data to specified destination

`quilt export USER/PACKAGE [DEST] --force` Overwrite files at destination

### `quilt export USER/PACKAGE [DEST] [--symlinks]`

Export data with symbolic links to reduce disk footprint.

If a node references raw (file) data, symbolic links may be used instead of copying data when exporting.

#### *Caution when using symbolic links*

* When using any OS
  * If a file is edited, it may corrupt the local quilt repository. Preventing this is up to the user.
* When using Windows
  * Symbolic links may not be supported
  * Symbolic links may require special permissions
  * Symbolic links may require administrative access (even if an administrator has the appropriate permissions)


---

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