=======================
Getting Started
=======================

.. contents:: Table of Contents
   :depth: 2
   :local:
   :backlinks: none

Login to VDJServer
----------------------------

VDJServer requires a user account to create projects, upload sequencing files, and
perform immune repertoire analysis. The user account ensures that your data stays
private until you are ready to publish.

A user account is not required to search the AIRR Data Commons and
download published studies from the :ref:`Community Data Portal <CommunityDataPortal>`.

VDJServer utilizes 3rd party identity providers such as Google, GitHub, ORCID, or
supported universities and institutions. A new username and password is not required.
However, you need to perform a one-time setup to :ref:`Connect Account <ConnectAccount>`
before logging in.

To login to VDJServer, go to the `VDJServer <https://vdjserver.org>`_ website with your web
browser as shown in the figure below.

.. figure:: user_images/home.png

Click on the "Login with ..." button, and you will be taken to a Tapis options
page that provides a number of login options.

.. figure:: user_images/login_options.png

Select the appropriate option for the account you have connected to
VDJServer. Perform authentication with your 3rd party account to
complete the login process. Upon successful authentication, the My
Projects page will be shown.

VDJServer saves a user token in your browser for convenience. This allows the browser
to skip the login process, but the token is only valid for a short period of time, usually
a few hours, after which it expires and you will need to authenticate again. If you do not
want those tokens to be saved in your browser, use the incognito or private-browsing
feature of your browser, and the token will deleted when you close the browser window.

.. figure:: user_images/my_projects.png

.. _ConnectAccount:

Connect Account to VDJServer
----------------------------

VDJServer does not require you to setup a new account with a username
and password. Instead, you use an existing 3rd party account like
Google, GitHub, ORCID, or your university/institution account. Connecting your
account to VDJServer requires a few one-time steps.

Click on the appropriate link below for instructions on connecting your account to VDJServer.

.. toctree::
   :maxdepth: 1

    Connect University Account using Globus <login_with_institution>
    Connect Google Account using Globus <login_with_google>
    Connect ORCID Account using Globus <login_with_orcid>
    Connect GitHub Account <login_with_github>

Send Feedback
-----------------------

Verification Check, resend email
Send Feedback

Create a New Project
----------------------
.. figure:: user_images/create_new_project.png
.. figure:: user_images/create_new_project_fields.png
.. figure:: user_images/save_new_projects.png
.. figure:: user_images/edit_project_metadata.png
.. figure:: user_images/save_project_metadata.png
.. figure:: user_images/revert_project_metadata_edits.png
.. figure:: user_images/project_metadata_edits_reverted.png
.. figure:: user_images/add_users_to_project.png
.. figure:: user_images/user_added_to_the_project.png
.. figure:: user_images/remove_user_from_project.png

Upload Files
---------------

.. figure:: user_images/upload_files_1.png
.. figure:: user_images/upload_files_2.png
.. figure:: user_images/upload_files_3.png
.. figure:: user_images/upload_files_4.png
.. figure:: user_images/upload_files_complete.png
.. figure:: user_images/saved_all_files.png

.. figure:: user_images/pair_files.png
.. figure:: user_images/pairing_complete.png
.. figure:: user_images/save_paired_files.png

Metadata Entry
--------------

.. figure:: user_images/export_subject_metadata.png
.. figure:: user_images/subject_metadata_table.png
.. figure:: user_images/subject_metadata_import.png
.. figure:: user_images/choose_subject_metadata_file.png
.. figure:: user_images/subject_metadata_imported.png
.. figure:: user_images/edit_subject_details.png

.. figure:: user_images/sample_processing_metadata_export.png
.. figure:: user_images/sample_processing_metadata_table.png
.. figure:: user_images/sample_processing_metadata_import.png
.. figure:: user_images/choose_sample_processing_metadata_file.png
.. figure:: user_images/sample_processing_metadata_imported.png
.. figure:: user_images/sample_processing_metadata_edit.png

Run Analysis Jobs
---------------------

Share Your Data
---------------

Publish Your Study
------------------

Tutorials, examples and workflows
---------------------------------