> 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/precompiled-binary.md). # Precompiled Binary [View full source code on GitHub](https://github.com/dnanexus/dnanexus-example-applets/tree/master/Tutorials/bash/samtools_count_binary_sh) ## Precompiling a Binary In this applet, the SAMtools binary was precompiled on an Ubuntu machine. A user can do this compilation on an Ubuntu machine of their own, or they can use the Cloud Workstation app to build and compile a binary. On the Cloud Workstation, the user can download the SAMtools source code and compile it in the worker environment, ensuring that the binary runs on future workers. See [Cloud Workstation](https://platform.dnanexus.com/app/cloud_workstation) in the App library for more information. ## Resources Directory The SAMtools precompiled binary is placed in the `/resources/` directory. Any files found in the `resources/` directory are packaged, uploaded to the Platform, and then extracted into the root directory `/` of the worker. In this case, the `resources/` dir is structured as follows: ``` ├── Applet dir │ ├── src │ ├── dxapp.json │ ├── resources │ ├── usr │ ├── bin │ ├── < samtools binary > ``` When this applet is run on a worker, the `resources/` directory is placed in the worker's root directory `/`: ``` / ├── usr │ ├── bin │ ├── < samtools binary > ├── home │ ├── dnanexus │ ├── applet script ``` The SAMtools command is available because the respective binary is visible from the default `$PATH` variable. The directory `/usr/bin/` is part of `$PATH`, so the script can reference the `samtools` command directly: ```shell samtools view -c "${mappings_bam_name}" > "${mappings_bam_prefix}.txt" ``` --- # 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 dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/precompiled-binary.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. 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.