Studios getting started guide #479

llewellyn-sl · 2025-02-18T19:44:33Z

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…dio types

robnewman

Amazing work! Super close - just some consistency issues and formatting. Also, swear jar for a couple of "Data studios" :)

platform_versioned_docs/version-24.3/getting-started/studios.mdx

robnewman · 2025-02-20T21:50:21Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+          - conda
+        ```
+
+- Select **Add** or choose to **Add and start** the studio immediately.


Suggested change

- Select **Add** or choose to **Add and start** the studio immediately.

- Select **Add** or choose to **Add and start** the studio session immediately.

robnewman · 2025-02-20T21:50:33Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+        ```
+
+- Select **Add** or choose to **Add and start** the studio immediately.
+- If you chose to **Add** the studio in the preceding step, select **Connect** in the options menu to open the studio in a new browser tab. 


Suggested change

- If you chose to **Add** the studio in the preceding step, select **Connect** in the options menu to open the studio in a new browser tab.

- If you chose to **Add** the studio session in the preceding step, select **Connect** in the options menu to open the session in a new browser tab.

robnewman · 2025-02-20T21:50:48Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+
+- Select **Add** or choose to **Add and start** the studio immediately.
+- If you chose to **Add** the studio in the preceding step, select **Connect** in the options menu to open the studio in a new browser tab. 
+- Once inside the studio, run `code.` to be able to use the clipboard.


Suggested change

- Once inside the studio, run `code.` to be able to use the clipboard.

- Once inside the studio, run `code.` to use the clipboard.

robnewman · 2025-02-20T21:51:08Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+- If you chose to **Add** the studio in the preceding step, select **Connect** in the options menu to open the studio in a new browser tab. 
+- Once inside the studio, run `code.` to be able to use the clipboard.
+
+#### Run nf-core/fetchngs with Conda 


Same question about heading level

robnewman · 2025-02-20T21:51:12Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+nextflow run nf-core/fetchngs -profile test,conda --outdir ./nf-core-fetchngs-conda-out -resume
+```
+
+#### Write a Nextflow pipeline with nf-core tools 


Same question about heading level

Co-authored-by: Rob Newman <[email protected]> Signed-off-by: Llewellyn vd Berg <[email protected]>

gwright99

Reviewed and commented as requested. Not explicitly asking for changes / approving since I'm tangential to your publication timeline.

gwright99 · 2025-02-21T14:04:01Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+toc_max_heading_level: 3
+---
+
+[Studios](../data_studios/index.mdx) allows users to host a variety of container images directly in Seqera Platform compute environments for analysis using popular environments including Jupyter (Python) and RStudio notebooks (R), Visual Studio Code IDEs, and Xpra remote desktops. Each studio session provides a dedicated interactive environment that encapsulates the live environment.


Add hyperlinks? I didn't know what Xpra was when I first heard it being talked about.

gwright99 · 2025-02-21T14:04:42Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+:::info[**Prerequisites**]
+You will need the following to get started:
+
+- Valid credentials for your cloud storage account and compute environment


Link to Credentials page in general docs?

gwright99 · 2025-02-21T14:06:38Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+
+### Jupyter: Python-based visualization of protein structure prediction data 
+
+Studios and Jupyter notebooks enable interactive analysis using Python libraries and tools. For example, PyMOL is a powerful tool used for visualizing and comparing structures produced by workflows such as [nf-core/proteinfold](https://nf-co.re/proteinfold/1.1.1), a bioinformatics best-practice analysis pipeline for protein 3D structure prediction. This section demonstrates how to create an AWS Batch compute environment, add the nf-core AWS megatests public proteinfold data to your workspace, create a Jupyter studio, and run the provided Python script to produce interactive composite 3D images of the H1065 sequence. 


I would remove the starting "Studios and". ASAIK 1st paragraph isn't dependent on Studios.

gwright99 · 2025-02-21T14:07:25Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+
+#### Create an AWS Batch compute environment 
+
+Studios requires an AWS Batch compute environment. If you do not have an existing compute environment available, create one with the following attributes:


Link to the Forge / Manual CE instructions for those who don't know how to do it?

gwright99 · 2025-02-21T14:08:17Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+
+#### Add data using Data Explorer
+
+For the purposes of this guide, add the proteinfold results (H1065 sequence) from the nf-core AWS megatests S3 bucket to your workspace using Data Explorer:


Link to the prefix or is assumption everyone knows what this is?
Nevermind, I see it's 2 lines down.

gwright99 · 2025-02-21T14:25:31Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+
+#### Perform the analysis and explore results
+
+1. Configure the RStudio environment with installed packages, including [ShinyNGS](https://github.com/pinin4fjords/shinyngs):


I have no familiarity with R. Leaving this section to Florian's expert eye for review.

gwright99 · 2025-02-21T14:27:01Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+        ```yaml 
+        channels:
+          - conda-forge
+          - bioconda


Any specific reason why conda is being used over pip here? Worth calling out why?

gwright99 · 2025-02-21T14:28:38Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+To use your own data for interactive analysis, see [Add a cloud bucket](./quickstart-demo/add-data.mdx#add-a-cloud-bucket) for instructions to add your own public or private cloud bucket. 
+:::
+
+#### Create an Xpra studio 


Isn't the whole "killer feature" about XPRA the ability for multiple people to collaborate in the container within the same session? If I'm right, this seems like something you'd want to call out beyond the solo interaction steps currently documented.

The killer feature of Xpra is also that it's a whole remote desktop with a GUI.

gwright99 · 2025-02-21T14:29:45Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+1. Search for PCSK9 and zoom into one of the exons of the gene. A coverage graph and reads should be shown, as below:
+    ![BAM file view](./_images/xpra-data-studios-IGV-view-bam.png)
+
+### VS Code: Create an interactive Nextflow developer environment


Does there need to be any text here that specifically talks about the Nextflow VS Code plugin?

i.e. "it'll work, you should use it" vs "omg, don't even think about trying that right now"

gwright99 · 2025-02-21T14:31:36Z

platform_versioned_docs/version-24.3/getting-started/studios.mdx

+1. Search for PCSK9 and zoom into one of the exons of the gene. A coverage graph and reads should be shown, as below:
+    ![BAM file view](./_images/xpra-data-studios-IGV-view-bam.png)
+
+### VS Code: Create an interactive Nextflow developer environment


IIRC VS Code has about a bazillion ways to import user preferences / configurations. Does the tutorial need to consider this angle (e.g. if I have a very customized local VS Code for executing my workflows and I now want to port this to a DS session, I assume I'd want my customizations to come with me?

llewellyn-sl added 4 commits February 17, 2025 20:29

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…dio types

VS Code instructions

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llewellyn-sl requested review from robnewman, FloWuenne and christopher-hakkaart February 20, 2025 16:30

llewellyn-sl added 3 commits February 20, 2025 18:31

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Co-authored-by: Rob Newman <[email protected]> Signed-off-by: Llewellyn vd Berg <[email protected]>

Update platform_versioned_docs/version-24.3/getting-started/studios.mdx

5deef93

Co-authored-by: Rob Newman <[email protected]> Signed-off-by: Llewellyn vd Berg <[email protected]>

gwright99 reviewed Feb 21, 2025

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Studios getting started guide #479

Studios getting started guide #479

llewellyn-sl commented Feb 18, 2025

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	- Select Add or choose to Add and start the studio immediately.
	- Select Add or choose to Add and start the studio session immediately.

	- If you chose to Add the studio in the preceding step, select Connect in the options menu to open the studio in a new browser tab.
	- If you chose to Add the studio session in the preceding step, select Connect in the options menu to open the session in a new browser tab.

	- Once inside the studio, run `code.` to be able to use the clipboard.
	- Once inside the studio, run `code.` to use the clipboard.


		### Jupyter: Python-based visualization of protein structure prediction data

		Studios and Jupyter notebooks enable interactive analysis using Python libraries and tools. For example, PyMOL is a powerful tool used for visualizing and comparing structures produced by workflows such as [nf-core/proteinfold](https://nf-co.re/proteinfold/1.1.1), a bioinformatics best-practice analysis pipeline for protein 3D structure prediction. This section demonstrates how to create an AWS Batch compute environment, add the nf-core AWS megatests public proteinfold data to your workspace, create a Jupyter studio, and run the provided Python script to produce interactive composite 3D images of the H1065 sequence.


		#### Create an AWS Batch compute environment

		Studios requires an AWS Batch compute environment. If you do not have an existing compute environment available, create one with the following attributes:


		#### Add data using Data Explorer

		For the purposes of this guide, add the proteinfold results (H1065 sequence) from the nf-core AWS megatests S3 bucket to your workspace using Data Explorer:


		#### Perform the analysis and explore results

		1. Configure the RStudio environment with installed packages, including [ShinyNGS](https://github.com/pinin4fjords/shinyngs):

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llewellyn-sl commented Feb 18, 2025

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netlify bot commented Feb 18, 2025 •

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