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Fix spacing and other minor issues
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llewellyn-sl committed Feb 21, 2025
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16 changes: 3 additions & 13 deletions platform_versioned_docs/version-24.3/getting-started/studios.mdx
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Expand Up @@ -24,7 +24,7 @@ You will need the following to get started:
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.

:::note
This script and instructions can also be used to visualize the structures from the results of nf-core/proteinfold runs with your own public or private data.
This script and instructions can also be used to visualize the structures from nf-core/proteinfold runs performed with your own public or private data.
:::

#### Create an AWS Batch compute environment
Expand Down Expand Up @@ -67,7 +67,6 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
- Select the latest **Jupyter** container image template from the list.
- Optional: Enter a unique name and description for the data studio.
- Check **Install Conda packages** and paste the following Conda environment YAML snippet:

```yaml
channels:
- schrodinger
Expand All @@ -82,8 +81,6 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
- biopython==1.85
- mdtraj==1.10.3
```
- Confirm the data studio details in the **Summary** tab.
- 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.
Expand Down Expand Up @@ -334,7 +331,7 @@ Studios requires an AWS Batch compute environment. If you do not have an existin
- **Region**: To reduce costs, your compute environment should be in the same region as your data. To browse the 1000 Genomes public data optimally, select **us-east-1**.
- **Provisioning model**: Use **On-demand** EC2 instances.
- Studios does not support AWS Fargate. Do not enable **Use Fargate for head job**.
- At least 2 available CPUs .
- At least 2 available CPUs.

#### Add data using Data Explorer

Expand Down Expand Up @@ -367,7 +364,6 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
- Select the latest **Xpra** container image template from the list.
- Optional: Enter a unique name and description for the studio.
- Check **Install Conda packages** and paste the following into the YML field:

```yaml
channels:
- conda-forge
Expand All @@ -376,7 +372,6 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
- igv
- samtools
```
- 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.
Expand All @@ -385,11 +380,8 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
1. In the Xpra terminal, run `igv` to open IGV desktop.
1. In IGV, change the genome version to hg19.
1. Select **File**, then **Load from file**, then navigate to `/workspace/data/xpra-1000Genomes/phase3/data/HG00096/high_coverage_alignment` and select the `.bai` file, as shown below:

![Load BAM file in IGV desktop](./_images/xpra-data-studios-IGV-load-bam.png)

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
Expand All @@ -403,7 +395,7 @@ Studios requires an AWS Batch compute environment. If you do not have an existin
- **Region**: To reduce costs, your compute environment should be in the same region as your data. To use the iGenomes public data bucket that contains the nf-core/fetchngs `test` profile data, select **eu-west-1**.
- **Provisioning model**: Use **On-demand** EC2 instances.
- Studios does not support AWS Fargate. Do not enable **Use Fargate for head job**.
- At least 4 available CPUs.
- At least 4 available CPUs and 16384 MB memory (RAM).

#### Add data using Data Explorer

Expand Down Expand Up @@ -432,7 +424,6 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
- Select the latest **VS Code** container image template from the list.
- Optional: Enter a unique name and description for the studio.
- Check **Install Conda packages** and paste the following into the YML field:

```yaml
channels:
- conda-forge
Expand All @@ -442,7 +433,6 @@ From the **Data Studios** tab, select **Add a data studio** and complete the fol
- nf-core
- conda
```

- 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.
Expand Down

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