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Update readme for instructions, correct links #28

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65 changes: 34 additions & 31 deletions README.md
Original file line number Diff line number Diff line change
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# DANDI Client
# LINC Brain Client

[![Tests](https://github.com/dandi/dandi-cli/workflows/Tests/badge.svg)](https://github.com/dandi/dandi-cli/actions?query=workflow%3ATests)
[![codecov.io](https://codecov.io/github/dandi/dandi-cli/coverage.svg?branch=master)](https://codecov.io/github/dandi/dandi-cli?branch=master)
[![Tests](https://github.com/lincbrain/linc-cli/workflows/Tests/badge.svg)](https://github.com/lincbrain/linc-cli/actions?query=workflow%3ATests)
[![codecov.io](https://codecov.io/github/lincbrain/linc-cli/coverage.svg?branch=master)](https://codecov.io/github/lincbrain/linc-cli?branch=master)
[![Conda](https://anaconda.org/conda-forge/dandi/badges/version.svg)](https://anaconda.org/conda-forge/dandi)
[![Gentoo (::science)](https://repology.org/badge/version-for-repo/gentoo_ovl_science/dandi-cli.svg?header=Gentoo%20%28%3A%3Ascience%29)](https://repology.org/project/dandi-cli/versions)
[![GitHub release](https://img.shields.io/github/release/dandi/dandi-cli.svg)](https://GitHub.com/dandi/dandi-cli/releases/)
[![PyPI version fury.io](https://badge.fury.io/py/dandi.svg)](https://pypi.python.org/pypi/dandi/)
[![Documentation Status](https://readthedocs.org/projects/dandi/badge/?version=latest)](https://dandi.readthedocs.io/en/latest/?badge=latest)

The [DANDI Python client](https://pypi.org/project/dandi/) allows you to:
The [LINC Brain Python client](https://pypi.org/project/lincbrain-cli/) allows you to:

* Download `Dandisets` and individual subject folders or files
* Download `Datasets` and individual subject folders or files
* Validate data to locally conform to standards
* Organize your data locally before upload
* Upload `Dandisets`
* Interact with the DANDI archive's web API from Python
* Delete data in the DANDI archive
* Perform other auxiliary operations with data or the DANDI archive
* Upload `Datasets`
* Interact with the LINC Brain archive's web API from Python
* Delete data in the LINC Brain archive
* Perform other auxiliary operations with data or the LINC Brain archive

**Note**: This project is under heavy development. See [the issues log](https://github.com/dandi/dandi-cli/issues) or
[Work-in-Progress (WiP)](https://github.com/dandi/dandi-cli/pulls).
**Note**: This project is under heavy development. See [the issues log](https://github.com/linc/linc-cli/issues) or
[Work-in-Progress (WiP)](https://github.com/linc/linc-cli/pulls).

## Installation

DANDI Client releases are [available from PyPI](https://pypi.org/project/dandi)
and [conda-forge](https://anaconda.org/conda-forge/dandi). Install them in your Python (native, virtualenv, or
LINC Brain Client releases are [available from PyPI](https://pypi.org/project/lincbrain-cli)
and [conda-forge](https://anaconda.org/conda-forge/lincbrain-cli). Install them in your Python (native, virtualenv, or
conda) environment via

pip install dandi
pip install lincbrain-cli

or

conda install -c conda-forge dandi
conda install -c conda-forge lincbrain-cli


## CLI Tool

This package provides a command line utility with a basic interface
to help you prepare and upload your data to, or obtain data from, the [DANDI archive](http://dandiarchive.org).
to help you prepare and upload your data to, or obtain data from, the [LINC Brain archive](http://lincbrain.org).


```bash
$> dandi
Usage: dandi [OPTIONS] COMMAND [ARGS]...
$> lincbrain
Usage: lincbrain [OPTIONS] COMMAND [ARGS]...

A client to support interactions with DANDI archive
(http://dandiarchive.org).
A client to support interactions with LINC Brain archive
(https://lincbrain.org).

To see help for a specific command, run

dandi COMMAND --help
lincbrain COMMAND --help

e.g. dandi upload --help
e.g. lincbrain upload --help

Options:
--version
Expand All @@ -62,23 +62,26 @@ Options:
--help Show this message and exit.

Commands:
delete Delete dandisets and assets from the server.
delete Delete datasets and assets from the server.
digest Calculate file digests
download Download a file or entire folder from DANDI.
instances List known Dandi Archive instances that the CLI can...
ls List .nwb files and dandisets metadata.
move Move or rename assets in a local Dandiset and/or on...
download Download a file or entire folder from LINC Brain Archive.
instances List known LINC Brain Archive instances that the CLI can...
ls List .nwb files and datasets metadata.
move Move or rename assets in a local Dataset and/or on...
organize (Re)organize files according to the metadata.
shell-completion Emit shell script for enabling command completion.
upload Upload Dandiset files to DANDI Archive.
validate Validate files for NWB and DANDI compliance.
upload Upload Dataset files to LINC Brain Archive.
validate Validate files for NWB and LINC Brain compliance.
validate-bids Validate BIDS paths.
```
Run `dandi --help` or `dandi <subcommand> --help` (e.g. `dandi upload --help`) to see manual pages.
Run `lincbrain --help` or `lincbrain <subcommand> --help` (e.g. `lincbrain upload --help`) to see manual pages.

## Resources

* To learn how to interact with the DANDI archive and for examples on how to use the DANDI Client in various use cases,
The LINC Brain ecosystem is forked from the [DANDI Archive project](https://github.com/dandi). Resources there should point
you towards common questions encountered within the LINC Brain project.

* To learn how to interact with the LINC Brain Archive (e.g. a forked DANDI archive) and for examples on how to use the DANDI Client in various use cases,
see [the handbook](https://www.dandiarchive.org/handbook/)
(specifically the sections on using the CLI to
[download](https://www.dandiarchive.org/handbook/12_download/) and
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