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Updated screenshots in part 2 of TM
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jacobfh1 committed Nov 12, 2024
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17 changes: 12 additions & 5 deletions TeachingModule/AnalysisMSData_FragPipe.qmd
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Expand Up @@ -50,18 +50,25 @@ Simple analyses in **FragPipe** may only require 8 GB of RAM, while large-scale

In UCloud, the settings should look like this:

**SCREENSHOT HERE**
![](images/TeachingModuleInstructions/UCloud_settings.png){width=750 fig-align="center"}

Before submitting the job, it is also recommended to create a personal folder where you can store both the data and the results generated by **FragPipe**. You can follow the step-by-step guide below:
Before submitting the job, it is highly recommended to create a personal folder to securely store both your data and the results generated by **FragPipe**. Follow the step-by-step guide below for an effortless setup:

**SCREENSHOT HERE**
1. First, click on the vibrant blue `Add folder` button.
2. Next, select the exact directory you wish to mount, as illustrated below:

**CAUTION!!!**
![](images/TeachingModuleInstructions/AddFolder1.png){width=750 fig-align="center"}

Upon clicking, a window similar to the one below will appear. Here, you have the option to either create a specific folder within a particular drive in the workspace you’ve chosen or simply select the entire drive itself. In this example, the drive is labeled as `Home` and the workspace is `My workspace`.

![](images/TeachingModuleInstructions/AddFolder2.png){width=750 fig-align="center"}


::: {.callout-caution}
Make sure to allocate the right number of hours before submitting the job. If the time runs out, the job will be canceled, and all progress will be lost. However, you can always extend the job duration if more time is required after submission.

Time can pass quickly when working, so we recommend initially allocating 2 hours for the job. Now, we are ready to submit the job and launch the virtual environment of the **Proteomics Sandbox Application**.

:::

#### Download Data from the Paper

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