For this example, we select Sandbox RNAseq workshop.
At the bottom left corner, you will find your user ID, which you may need to provide once the course starts or for future collaborations, such as being added to other people’s projects. You can also find it on UCloud docs.
Then click on Apps in the left panel to investigate what tools and environments you can use (orange square). The easiest way to find Sandbox resources is to search via the toolbar (red circle). In this example, we’ll select the Genomics Sandbox (which will bring you to the submission screen).
Click on the app button to get into the settings window. First, we recommend reading the documentation of the app (step 2). Then, you can configure the app as shown below, or be provided with a configuration file made available in a workshop’s project folders (import parameters) which will take care of everything for you.
Wait to go through the queue. When the session starts, the timer begins to count down. In a couple of minutes, you should be able to open the interface through the button (Open interface) in a new window (refresh the window if needed).
Different apps might employ distinct development environments, so your interface experience could vary accordingly. If you’re utilizing an RStudio-based application, like the transcriptomics tool, your interface will launch in a new tab, resembling the image provided below. Simply navigate through the folders to locate and access the R Markdown notebooks.
If you are testing a JupyterLab-based application, such as the genomic app, your interface should look like in the image below. In this case, you will be working from JupyterLab. You can open Jupyter Notebooks (yellow square), R studio (blue square) or a terminal (black square) among others. In this case, the highlighted buttons (under Notebooks) have all the software and packages that you will need pre-installed (this is not the case with Python 3 to the left).
You can navigate through the different folders and start running the Python notebooks (orange square).
Links to download the material for this workshop here.
-High-Performance Computing (HPC) platforms are essential for large-scale data analysis. Therefore, we will be running our bulk RNA-seq analyses on one of the national HPC platforms. We will guide you through the setup process for using UCloud. For more details or to repeat the process on your own, you can also visit this website.
High-Performance Computing (HPC) platforms are essential for large-scale data analysis. Therefore, we will be running our bulk RNA-seq analyses on one of the national HPC platforms, UCloud.
For more details or to repeat the process on your own, you can also visit this website. - To review the course material, visit our website where you will find the content for all the lectures.
+- Zenodo link to download the material (slides, assignments, data, etc.) for this workshop here. - To get started with our transcriptomics app, follow the UCloud setup guidelines. - To run the nf-core RNAseq pipeline follow the instructions here
