IBA - Logging on to NeLS and finding course data

<center><img src="https://i.imgur.com/BWehQrf.png" alt="drawing" width="700"/></center> # IBA - Logging on to NeLS and finding course data :::success In this hands-on exercise, you will log in to the **NeLS Portal** and find the location of the exercise data you will be using during this course. You can access the **NeLS portal** at [https://nels.bioinfo.no/](https://nels.bioinfo.no/) ::: :::info :information_source: **Note:** Names of files, folders, commands, and other functionality elements will be highlighted through the exercises in the following way: `file_name_example.txt`. User specific (and thus variable) character strings as for example user_name will be written between `<` and `>` as `<user_name>` to indicate the meaning. ::: ## Access the NeLS portal :::success **NeLS** the Norwegian e-Infrastructure for Life Sciences, is an infrastructure for analysis, sharing and storage of Life Science data, such as high throughput genomics data. Access to the infrastructure is mainly through a web portal with an easy-to-use graphical interface that allow the user to manage the data in a project. The user will need **FEIDE** credentials to access the portal. Non-FEIDE users (eg. collaborators) can get access using a **NeLS idp** which can obtained by contacting the **ELIXIR Norway helpdesk**: <contact@bioinfo.no> ::: I. In a web browser go to the [NeLS portal](https://nels.bioinfo.no/) and press `Login` (upper right of your screen). II. If you are not already logged in to the system, you need to select your identity provider. For most of you this will be `Login with FEIDE identity`. Non-FEIDE users must select `Login with NeLS identity`. <center><img src="https://i.imgur.com/AM3M6nl.png" alt="drawing" width="800"/></center> III. Add your username and password when promted, and press `Log in`. <center><img src="https://i.imgur.com/2yZDulZ.png" alt="drawing" width="300"/></center> IV. First time visitors will need to accept **Terms of usage** in order to proceed. IV. You should now see you **Dashbord** inside the NeLS portal (Your personal dashboard will not have the same content as shown in the screen shot). <center><img src="https://i.imgur.com/hK76ChP.png" alt="drawing" width="800"/></center> :::info :information_source: **Main features in the NeLS portal** 1. Your total disk usage in NeLS Personal area (not including NeLS and SBI projects) 2. Important notifications 3. Overview of the most recent folders you have visited in NeLS 4. Your personal folder (and sub folders) 5. The NeLS projects that you have access to (in most cases these projects are shared with collaborators, all with different access permissions) 6. The StoreBioInfo projects that you have access to (in most cases these are long(er) term storage of corresponding NeLS projects, holding all the original data of a project) 7. Overview of available analysis workflows in usegalaxy.no 8. Contact the **ELIXIR Norway helpdesk** 9. Connection details for access to NeLS via the command line, Terms of use and Logout. (Also notice your NeLS ID number which is an identifier in the NeLS user database which is uniquely matched to your FEIDE user identity) ::: --- ## Create and delete folders in NeLS :::success In this part of the exercise, you will explore the folder structure in **NeLS**, create and delete folders. ::: I. Start by exploring the different pages in the **NeLS portal**. Go to your `Personal` folder. It should list all your personal folders and be empty if you are a first-time user II. Create a new folder by pressing `New folder` [1] III. In the pop-up window that appears, give the folder a name [2] and press `Save` <center><img src="https://i.imgur.com/4m60Nkk.png" alt="drawing" width="800"/></center> IV. You should see the folder appear in your `Personal` folder V. Delete the newly created folder by selecting it [1] and pressing `Delete Selected` [2] <center><img src="https://i.imgur.com/AaVHLA2.png" alt="drawing" width="800"/></center> VI. You should see the folder disappear from your `Personal` folder :::info :information_source: Notice that you are able to manage data (upload, download, etc.) directly in the portal. We will do this later in the course. ::: --- ## Locate the exercise data :::success Prior to this course we made a project named "**IBA_ELIXIR_2021**" and added all course participants to this shared project. In this part of the exercise, you will access this folder that contains all exerice data we will use. Users in shared project may have different roles. All roles have the permission to upload and download data. Only PIs, Data Managers or Power Users (or Helpdesk) can delete data. In "**IBA_ELIXIR_2021**" you have the role Normal user. You can only add data and folders, navigate and download. You are not able to delete data from a project. ::: I. Go to your `Project` folder. It should list all your project folders, including (and maybe only) the folder named `IBA_ELIXIR_2021` II. You should see your role in the project (in the example the role is PI) and what permissions that this role has [1] III. You should also be able to see who the other members of this shared project is by clicking on `Members` [2] <center><img src="https://i.imgur.com/KAooxjr.png" alt="drawing" width="800"/></center> IV. Click on `Members` and a new window appears V. If your role is PI, Data Manager or Power User (or Helpdesk) you have permissions to add new members to the project [1], change the role of other members [2], or remove members from the project [3] <center><img src="https://i.imgur.com/o94Rk5N.png" alt="drawing" width="800"/></center> VI. Go back to the overview of your projects, and enter the `IBA_ELIXIR_2021` by clicking on it. There should be both several files and subfolders in the `IBA_ELIXIR_2021` folder VII. Download the file named `test_download_NeLS.txt` to your local machine by clicking on the file and selecting `Save file to disk` in the pop-up window that appears :::success :+1: That was the end of this practical. :::