> For the complete documentation index, see [llms.txt](https://documentation.dnanexus.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash.md).

# Bash

- [Bash Helpers](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/bash-helpers.md): Learn to build an applet that performs a basic SAMtools count with the aid of bash helper variables.
- [Distributed by Chr (sh)](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/distributed-by-chr-sh.md)
- [Distributed by Region (sh)](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/distributed-by-region-sh.md)
- [SAMtools count](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/samtools-count.md)
- [TensorBoard Example Web App](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/tensorboard-example-web-app.md)
- [Git Dependency](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/git-dependency.md)
- [Mkfifo and dx cat](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/mkfifo-and-dx-cat.md)
- [Parallel by Chromosome (sh)](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/parallel-by-region-sh.md): This applet performs a basic SAMtools count on a series of sliced (by canonical chromosome) BAM files in parallel using wait (Ubuntu 14.04+).
- [Parallel xargs by Chr](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/parallel-xargs-by-chr.md): This applet slices a BAM file by canonical chromosome then performs a parallelized samtools view -c using xargs. Type man xargs for general usage information.
- [Precompiled Binary](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/precompiled-binary.md): This tutorial showcases packaging a precompiled binary in the resources/ directory of an app(let).
- [R Shiny Example Web App](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/r-shiny-example-web-app.md): This is an example web applet that shows how to build and run an R Shiny application on DNAnexus.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://documentation.dnanexus.com/getting-started/developer-tutorials/bash.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.