Merge pull request #285 from LRFreeborn/sratoolkit_guide

add sratoolkit_guide

docs/software/sratoolkit.md

@@ -0,0 +1,78 @@
+# 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. 
+
+
+
+