Logging on to NeLS and finding course data

<center><img src="https://i.imgur.com/sP7cyyX.png" alt="drawing" width="200"/></center> # Logging on to NeLS and finding course data <html> <div style="background-color: #f2f3f4"> 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/) </div> </html> <br/> :::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 <html> <div style="background-color: #f2f3f4"> **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> </div> </html> <br/> I. In a web browser go to the [NeLS portal](https://nels.bioinfo.no/) and press `Login` (upper right of your screen). <br/> 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`. <br/> <center><img src="https://i.imgur.com/AM3M6nl.png" alt="drawing" width="800"/></center> <br/> III. Add your username and password when promted, and press `Log in`. <br/> <center><img src="https://i.imgur.com/2yZDulZ.png" alt="drawing" width="300"/></center> <br/> IV. First time visitors will need to accept **Terms of usage** in order to proceed. <br/> IV. You should now see you **Dashbord** inside the NeLS portal. <br/> <center><img src="https://i.imgur.com/VsYrADh.png" alt="drawing" width="800"/></center> <br/> <html> <div style="background-color: #f2f3f4"> #### Main features in the NeLS portal 1. Important notifications 2. Your total disk usage in NeLS Personal area (not including NeLS and SBI projects) 3. Job Status; Submitted, In Progress, Succeeded, Failed 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. Help and Support; contacting the **ELIXIR Norway helpdesk** 7. Terms of Usage; purpose of NeLS, how your information is collected, data security, how long information is stored, how to request removal from NeLS, etc. 8. Link to ELIXIR Norway website. 9. Guide on NeLS, usegalaxy, and StoreBioInfo (long(er) term storage of corresponding NeLS projects, holding all the original data of a project) 10. Available analysis workflows in usegalaxy.no 11. Your profile on NelS; contains important informations such as connection details for access to NeLS via the command line, and NeLS ID (an identifier in the NeLS user database which is uniquely matched to your FEIDE user identity). </div> </html> --- ## Create and delete folders in NeLS <html> <div style="background-color: #f2f3f4"> In this part of the exercise, you will explore the folder structure in **NeLS**, create and delete folders. </div> </html> <br/> I. Start by exploring the different pages in the **NeLS portal**. Go to `NeLS Personal` section. It should list all your personal folders and be empty if you are a first-time user <br/> II. Create a new folder by clicking on the plus sign, it will say `Add folder` <center><img src="https://i.imgur.com/q7PawnC.png" alt="drawing" width="800"/></center> <br/> III. In the pop-up window that appears, give the folder a name and press `Save`. <br/> <center><img src="https://i.imgur.com/QtaQ7zI.png" alt="drawing" width="800"/></center> <br/> IV. You should see the folder appear in your `NeLS Personal` section. <br/> V. Delete the newly created folder by clicking on three dots (More Options icon) and pressing `Delete`. <br/> <center><img src="https://i.imgur.com/SyzsVOv.png" alt="drawing" width="800"/></center> <br/> VI. A pop up window will appear where you can click 'Delete' to confirm. <center><img src="https://i.imgur.com/BhBy0Ec.png" alt="drawing" width="800"/></center> <br/> VII. You should see the folder disappear from your `Personal` folder. You will see notification in green box, at the bottom of your screen, saying "delet_this was deleted successfully" <br/> :::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 <html> <div style="background-color: #f2f3f4"> Prior to this course we made a project named "**ELIXIR_online_course_2022**" 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 "**ELIXIR_online_course_2022**" 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. </div> </html> <br/> I. Go to `NeLS Projects` sections. It should list all your project folders, including (and maybe only) the folder named `ELIXIR_online_course_2022` <br/> II. You should see your role in the project. In the example, the role is PI. <br/> <center><img src="https://i.imgur.com/ZQFJrV5.png" alt="drawing" width="800"/></center> <br/> III. Hovering over the role term (e.g. PI, data manager) will give information on what permissions this role has. <br/> <center><img src="https://i.imgur.com/PGzr6xf.png" alt="drawing" width="800"/></center> <br/> <br/> IV. You can see who the other members of this shared project by clicking on 'More options' icon (three dots), and then click on 'NeLS Project Information'. It also gives you details about the project such as when it was created and disk usage. <br/> <center><img src="https://i.imgur.com/NcQQ37f.png" alt="drawing" width="800"/></center> <br/> V. If your role is PI, Data Manager or Power User (or Helpdesk), you have permissions to add new members to the project - for this, you will find 'Add Member' button on right. You can also change the role of other members, or remove members from the project - to be able to do this, click on 'More options' icon (three dots) before member's name and select either 'Edit' or 'Remove'. If you are unable to find a name in the list, write a name in 'Search Text' field. <br/> <center><img src="https://i.imgur.com/vDsydSK.png" alt="drawing" width="800"/></center> <br/> VI. Go back to the 'NeLS Prpjects' section, and enter the `ELIXIR_online_course_2022` by clicking on it. There should be both several files and subfolders in the `ELIXIR_online_course_2022` folder. <br/> VII. Download the file named `test_download_NeLS.txt` to your local machine by clicking on the file, then select `Download` in the pop-up window that appears. The other way to download the file is by clicking on 'More options' icon (three dots) and select 'Download' button. <br/> :::success :+1: That was the end of this practical. Please remember to type "**done**" in the chat. :::