# SRA Toolkit on Alpine

SRA Toolkit provides tools for downloading data, converting data into SRA format, and extracting SRA data into other data formats.

## Loading the Module

From an Alpine compute node:
``` bash
module load sra-toolkit
```

## Configuring SRA Toolkit 

Some SRA Toolkit commands, such as `fasterq-dump`, generate large temporary files that are approximately the size of the final output file(s). SRA Toolkit writes these 
temporary, 
or cache, files to `/home/$USER`. CURC `/home/$USER` is limited to 2 GB, so users must direct this cache somewhere else. We recommend `/scratch/alpine`, since each user has up 
to 10 TB and it is automatically purged every 90 days. 

Users should redirect the cache using SRA Toolkit's `vdb-config -i`. Settings are saved and persist across sessions, so this is only necessary the first time you run SRA 
Toolkit on CURC Alpine.

Before running the configuration command, create an `sra` directory in your scratch space.

``` bash
mkdir /scratch/alpine/$USER/sra
```
This directory must be empty, so don't add anything to it.

Now start the `vdb-config` program.

``` bash
module load sra-toolkit
vdb-config -i
```

A configuration window will open in your terminal.

![](./software_images/config_window.png) 

Navigate to the CACHE tab using your tab key. Press enter when the red cursor lands on CACHE. Keep pressing tab until the red cursor is on `location of user-repository: [ 
choose ]`. 

![](./software_images/navigating_to_cache_location.png)

Press enter. A `select directory` window will appear.

![](./software_images/file_navigator.png)

Tab over to `[ Goto ]` and press enter. A new pop-up window will appear. Delete the existing file path (e.g., `/home/lrf20@xsede.org`) using your delete/backspace key and enter 
the absolute path of your new `sra` cache directory. 

`vdb-config -i` requires your specified directory to exist (it won't create it for you) and be an *empty* directory. You must also have read/write permissions. The program will 
not save your selection if these criteria aren't met. 

![](./software_images/select_new_cache_dir_2.png)

Tab over to `[ OK ]` and press enter. Confirm the directory listed at the top of the 'select directory' window says `/scratch/alpine/<your username/sra>` Tab over to `[ OK ]` 
and press enter.

![](./software_images/see_new_path.png)

A window asking you to confirm the change will appear. Select `[ yes ]`.

![](./software_images/confirm_new_dir.png)

Tab over to `[ save ]` and press enter. A window will appear telling you the changes have been saved successfully. Select `[ ok ]`.

Tab to `[ exit ]` and press enter.

SRA Toolkit is ready for use!

## Common SRA Toolkit Issues

- Download errors are common with commands like `prefetch`, `fasterq-dump`, and `hisat2`, as the NCBI SRA server can be overwhelmed.