# Git Dependency

[View full source code on GitHub](https://github.com/dnanexus/dnanexus-example-applets/tree/master/Tutorials/bash/samtools_count_git_sh)

## What does this applet do?

This applet performs a basic SAMtools count of alignments present in an input BAM.

## Prerequisites

The app must have network access to the hostname where the git repository is located. In this example, `access.network` is set to:

```json
"access": {
  "network": ["github.com"]
}
```

To learn more about `access` and `network` fields see [Execution Environment Reference](https://documentation.dnanexus.com/developer/apps/execution-environment).

## How is the SAMtools dependency added?

SAMtools is cloned and built from the [SAMtools GitHub](https://github.com/samtools/samtools) repository. The following is a closer look at the `dxapp.json` file's `runSpec.execDepends` property:

```json
  "runSpec": {
 ...
    "execDepends": [
        {
          "name": "htslib",
          "package_manager": "git",
          "url": "https://github.com/samtools/htslib.git",
          "tag": "1.3.1",
          "destdir": "/home/dnanexus"
        },
        {
          "name": "samtools",
          "package_manager": "git",
          "url": "https://github.com/samtools/samtools.git",
          "tag": "1.3.1",
          "destdir": "/home/dnanexus",
          "build_commands": "make samtools"
        }
    ],
...
  }
```

The `execDepends` value is a JSON array of dependencies to resolve before the applet source code is run. In this applet, the git fetch dependencies for `htslib` and SAMtools are specified. Dependencies resolve in the order listed. Specify `htslib` first, before the SAMtools `build_commands`, because newer versions of SAMtools depend on `htslib`. An overview of each property in the git dependency:

* `package_manager` - Details the type of dependency and how to resolve. [supplementary details](https://documentation.dnanexus.com/developer/apps/execution-environment).
* `url` - Must point to the server containing the repository. In this case, a GitHub URL.
* `tag`/`branch` - Git tag/branch to fetch.
* `destdir` - Directory on worker to which the git repository is cloned.
* `build_commands` - Commands to build the dependency, run from the repository `destdir`. In this example, `htslib` is built when SAMtools is built, so only the SAMtools entry includes `build_commands`.

The `build_commands` are executed from the `destdir`. Use `cd` when appropriate.

## How is SAMtools called in the `src` script?

Because `"destdir": "/home/dnanexus"` is set in `dxapp.json`, the git repository is cloned to the same directory from which the script executes. The example directory's structure:

```
├── home
│   ├── dnanexus
│       ├── < app script >
│       ├── htslib
│       ├── samtools
│           ├── < samtools binary >
```

The SAMtools command in the app script is `samtools/samtools`.

## Applet Script

```shell
main() {
  set -e -x -o pipefail

  dx download "$mappings_bam"

  count_filename="${mappings_bam_prefix}.txt"
  readcount=$(samtools/samtools view -c "${mappings_bam_name}")
  echo "Total reads: ${readcount}" > "${count_filename}"

  counts_txt=$(dx upload "${count_filename}" --brief)
  dx-jobutil-add-output counts_txt "${counts_txt}" --class=file
}
```

You can build SAMtools in a directory that is on the `$PATH` or add the binary directory to `$PATH`. Keep this in mind for your app(let) development.


---

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