<center><img src="https://i.imgur.com/sP7cyyX.png" alt="drawing" width="200"/></center> # Logging in to usegalaxy.no, data transfer and deleting data <html> <div style="background-color: #f2f3f4"> In this hands-on exercise, you will log in to **usegalaxy.no**, get to know the web interface and transfer data to and from **usegalaxy.no**. You will also perform some simple manipulations of your data and delete data. You can access the **usegalaxy.no** at [https://usegalaxy.no/](https://usegalaxy.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. ::: ## Login to usegalaxy.no and get to know the user interface <html> <div style="background-color: #f2f3f4"> Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. **usegalaxy.no** is a national Galaxy server for life science data hosted and supported by ELIXIR Norway. **usegalaxy.no** is accessible to all Norwegian users and their collaborators - just like NeLS. 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 [usegalaxy.no](https://usegalaxy.no/). If not already logged in, you will be asked to login by pressing the `NeLS sign in` button and adding your login credentials. <br/> <center><img src="https://i.imgur.com/dkh1ymS.png" alt="drawing" width="400"/></center> <center><img src="https://i.imgur.com/DSPImhS.png" alt="drawinng" width="800"/></center> <br/> II. For first time users, and users with no data in usegalaxy.no the front page should look like below <br/> <center><img src="https://i.imgur.com/UrOg5Dn.png" alt="drawing" width="800"/></center> <br/> III. If you have used usegalaxy.no before, you should start a "fresh" history by pressing the `+` sign in the **History view** (upper right of the screen) <br/> IV. Rename your history by pressing on the current name (`Unnamed history`). Give the history any name you prefer, and press `enter` <br/> <center><img src="https://i.imgur.com/NX1uQ5b.png" alt="drawing" width="200"/></center> <br/> V. Galaxy allow you to add custom tags and annotations to you histories (and datasets) that can make it easier to search/sort your histories, and describe the content. Add a tag [1] and an annotation [2] to your history <br/> <center><img src="https://i.imgur.com/4VZY7EA.png" alt="drawing" width="800"/></center> <br/> ## Import data from NeLS <html> <div style="background-color: #f2f3f4"> <br/> **usegalaxy.no** is directly connected to your data storage in **NeLS**. This exclude the need for local copy of your data. You can simply transfer data directly between **usegalaxy.no** and **NeLS**. </div> </html> <br/> I. In the **Tools** menu under the `Get Data` section, press `Get files from NeLS storage` [1]. This should redirect you to the **NeLS portal** (might require login) <br/> II. Once inside the **NeLS portal**, browse to the subfolder `intro_usegalaxy` (The path is: `/Projects/ELIXIR_online_course_2021`) [2] <br/> III. Select the files named `test_NeLS_import.txt`and `test_NeLS_DNAimport.txt`, and press `Send to Galaxy` [3] <br/> <center><img src="https://i.imgur.com/j5viaNn.png" alt="drawing" width="800"/></center> <br/> IV. You will be redirected back to **usegalaxy.no** and the imported data should appear in your current history <br/> V. When importing data from **NeLS**, you cannot define the datatype (format). Preview the imported datasets by clicking on the file names [1]. Notice that both files are imported as `txt` [2], but that `test_NeLS_DNAimport.txt` is actually a `fasta file` [3] <br/> VI. Change the datatype (format) by pressing `Edit attributes`" [4]. In the **Main Galaxy** window select the `Datatype` tab [5] and start typing `fasta` [6]. You should be able to select the correct format from the drop-down menu. Finally, change the datatype [7]. In your history, the format should change to `fasta` <br/> <center><img src="https://i.imgur.com/a3Js5qC.png" alt="drawing" width="800"/></center> <br/> ## Export data from usegalaxy <html> <div style="background-color: #f2f3f4"> Dataset and histories can be exported from **usegalaxy.no** either to your local system or to the **NeLS storage**. Since **usegalaxy.no** is not meant for storage we encourage you to move your data when your analysis is done. First, you will run a simple tool that turn the fasta file into another dataset, so that we can export a different file than we imported. You will learn more about tools later in the course. </div> </html> <br/> I. In the **Tools** menu under the `FASTA/FASTQ` category [1] locate the tool `FASTA-to-Tabular`[2]. Select `test_NeLS_DNAimport.txt` as input [3] and press `Execute` to run the tool <br/> <center><img src="https://i.imgur.com/lBb3A2D.png" alt="drawing" width="800"/></center> <br/> II. Galaxy will run the tool and produce a new dataset. This will be listed at the top of your history and contain a tab-separated file with the fasta header in the first coloumn and the sequence in the second coloumn <br/> III. Click on the new dataset to expand the information that comes with it. Preview the file content and datatype. Press on `View details` [1]. Can you tell which **version of the tool** that was used and how much **memory it required**? <br/> IV. Dataset names produced by Galaxy are informative in that they describe the tool and the input data, but sometimes it can be useful to give it a different name. Rename the new dataset to `test_NeLS_export`by pressing `Edit attributes` [2]. Select `Attributes` [3], rename the dataset [4] and press `Save` [5] <br/> <center><img src="https://i.imgur.com/KbLZ6WY.png" alt="drawing" width="800"/></center> <br/> V. Download this file to your local system by pressing `Download` [1] and selecting to save the file to disk. <br/> VI. Download the complete history containing all datasets as a single file to disk by pressing `History options` [2] and selection `Export History to File` [3] <br/> VII. Finally, export the complete history as a single file to **NeLS** by selecting `Export History` under the `NeLS storage` section [4]. You will be redirected to the **NeLS portal** where you need to choose the destination folder [5] (shown here a random subfolder in the `Personal` folder). Since you do not have permissions to write to the shared project folder in **NeLS**, you need to export it into your `Personal` folder. Browse to your `Personal` folder (or a subfolder here) and press `Use current folder` [6]. <br/> VIII. You should be redirected back to **usegalaxy.no** where you can view the transfer progress (you might need to scroll down a bit in the **usegalaxy.no** main window). When the transfer is complete, the progression bar will turn green [7]. If you want to double check, you can open a new web browser and check that the file is present in the folder you chose in [5] <br/> <center><img src="https://i.imgur.com/nD7oQtn.png" alt="drawing" width="800"/></center> ## Sharing history in usegalaxy <html> <div style="background-color: #f2f3f4"> Dataset and histories can be shared with other users of **usegalaxy.no**. You can choose to share histories (or only datasets) with all users, a single user or via a url. Users you have shared the history with, can import it and continue working on their copy of your history. They will not have access to your personal history and cannot edit your version of the history. You can unshare the history at any time, but users that have imported the history will still have their copy of it. </div> </html> <br/> I. Press the `History option` and select `Share or Publish` [1] <br/> II. In the new window that appear, you have three options for sharing the history. Select `Make History Accessible via Link` [2] <br/> III. You sould get a url that you can share with other **usegalaxy.no** users [3]. This link can be disabled [4] <br/> IV. The option `Publish History` [5] will make the history accessible to all **usegalaxy.no** users via the `Shared data` menu, and `Share with a user` [6] allow you to share it with **usegalaxy.no** users via their **usegalaxy.no** users emails. <br/> <center><img src="https://i.imgur.com/1x2z5wv.png" alt="drawing" width="800"/></center> <br/> ## Importing shared history in usegalaxy.no <html> <div style="background-color: #f2f3f4"> Histories that have been shared by other users in **usegalaxy.no** can be imported from the `Shared Data`. </div> </html> <br/> I. Press the `Shared Data` and select `Histories` [1] <br/> II. From the list of shared histories, press on the history named `ELIXIR workshop history` [2]. <br/> III. In the new window that apperar, a short description of the history and the datasets are presented. Press the `+` sign [3] <br/> IV. You can now choose to import the history [4]. You can also rename the history before importing it <br/> V. The imported history will now be the active history [5] <br/> <center><img src="https://i.imgur.com/isYhyrg.png" alt="drawing" width="800"/></center> <br/> ## Importing history from NeLS in usegalaxy.no <html> <div style="background-color: #f2f3f4"> Histories can also be imported from a project in **NeLS** or your local machine - given that you have histories stored here. Export to local machine is not covered here, but it is very straight forward from the "**History option**" menu. </div> </html> <br/> I. Importing history from NeLS is done from the `History option`. Press `Import History` [1] under `NeLS Storage` <br/> II. You will be redirected to the **NeLS storage**. Browse to the history you exported to you personal folder earlier in this exercise, select the file [2] and press `Send to Galaxy`[3] <br/> III. You will be redirected back to **usegalaxy.no** and you can monitor the progress of the import [4]. The progress bar will turn green when the import is complete [5] <br/> IV. The name of the imported history will be `imported from archive: ....`. The history can be accessed by selecting `Histories` [6] under the **User**" menu. You can rename the history if you like. <br/> <center><img src="https://i.imgur.com/2SBoHsy.png" alt="drawing" width="800"/></center> <br/> ## Change between histories <html> <div style="background-color: #f2f3f4"> Normally you will accumulate histories in Galaxy. In this part of the exercise, you will move from the active history into another history, which will become the active history. </div> </html> <br/> I. You can access the overview of your histories two ways; by by selecting `Histories` [1] under the **"User"** menu or by pressing `View all histories` [2] in the "**History**" panel. <br/> II. Depending on which method you use, the list of you histories will be displayed in slightly different manner. <br/> III. You can change from the current history to any histories in the list by either selecting the history and click on `Switch` [3] or by clicking on `Switch to` [4] above the history you want to change to <br/> IV. The history you chose will become the active (current) history <br/> <center><img src="https://i.imgur.com/WNEgCmN.png" alt="drawing" width="800"/></center> <br/> ## Delete datasets and complete histories <html> <div style="background-color: #f2f3f4"> Galaxy offer multiple ways to delete datasets and histories, and you will try two of them in this exercise. The are two major types of deletion: 1. Delete datasets or histories - This option temporary delete data (basically just hide the data) 2. Permanently delete datasets or histories - This option permanently delete data from the disk NB! Even if you select to permanetly delete data, the avaliable space in your galaxy disk quota does not change before the “Trash bin” has been emptied. This will happen automatically every week. </div> </html> <br/> I. Make sure your current history is the history you imported from **NeLS** previously (if you didn't rename it, it should be called something that starts with `imported from archive: ....`) <br/> II. Select the dataset(s) you want to delete (temporary) by pressing `X` next to the dataset in your "**History**" panel [1]. The dataset should disappear from you history, but you still access it [2] <br/> III. You have only temporary deleted the data (equal to moving it to the trash bin on you computer), and it can be undeleted (moved back from trash bin), or permanently deleted by pressing `Permanently remove it from disk` [3] <br/> IV. Press `OK` to confirm the permanent deletion [4] <br/> V. You can still see traces of the dataset in your history [5], but the data in the file is deleted from the disk and you have freed up disk space:) <br/> <center><img src="https://i.imgur.com/WsL65bF.png" alt="drawing" width="800"/></center> <br/> VI. Similarly, you can temporary and permanently delete histories. Access the overview of your histories in either of two ways described earlier; by selecting `Histories` [1] under the "**User**" menu or by pressing `View all histories` [2] in the "**History**" panel <br/> VII. From the drop-down menu of the history you want to delete (still the imported history from NeLS named `imported from archive: ....`), press `Delete Permanently` [3]. If you chose the other history view, from the drop-down menu of the history you want to delete press `Purge` [4]. Both options will ask you to confirm the deletion, and both options will erase the data from disk. :::info :information_source: We strongly encourage that you copy your histories to NeLS and permanently delete data from usegalaxy.no when you are done with your data analysis. This will free up your personal disk space in usegalaxy.no ::: <br/> <center><img src="https://i.imgur.com/6LrbAtv.png" alt="drawing" width="800"/></center> <br/> :::success :+1: That was the end of this practical. Please remember to type "done" in the chat. :::