# DNAnexus

[DNAnexus](https://www.dnanexus.com/) supports WDL workflows through their `dx-toolkit` and `dxCompiler` tools. This guide demonstrates running the `02_download_collection_files.wdl` workflow, which typically takes 5-10 minutes to complete.

## Prerequisites

Before beginning, ensure you have the following:

* [A DNAnexus platform account (including free tier)](https://platform.dnanexus.com/register)
* Java 8 or higher
* Python 3.5 or higher
* Optional: cURL, [git](https://git-scm.com/downloads)

## Getting Started

The following software and workflows are required and will be installed and used as part of this tutorial:

* [02\_download\_collection\_files.wdl](https://raw.githubusercontent.com/DNAstack/dnastack-client-library-worked-examples/master/examples/wdl/02_download_collection_files.wdl)
* [dx-toolkit](https://docs.viral.ai/analysis/integrations/dnanexus/)
* [dxCompiler](https://github.com/dnanexus/dxCompiler)

## Getting the Example Workflow

**Clone with Git:**

```shell
git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git
```

**Or** [**Download**](https://github.com/DNAstack/dnastack-client-library-worked-examples/archive/refs/heads/master.zip) **and Unzip**

It is assumed that all commands will be run from the root directory of this repository on your local machine. From the directory where you’ve downloaded the examples repository:

```shell
git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git
```

#### Installing Required Tools

**Download dxCompiler:**

Download the latest version of `dxCompiler` by one of the following methods. This allows direct conversion and uploading of WDL workflows to DNAnexus.

#### Using cURL

```shell
curl -o dxCompiler.jar -L https://github.com/dnanexus/dxCompiler/releases/download/2.4.6/dxCompiler-2.4.6.jar
```

Or download from the releases page to the current directory and rename the file to `dxCompiler.jar`.

#### Install and initialize dx-toolkit

Download and initialize `dx-toolkit`. You will be prompted to log into your DNAnexus account.

```shell
pip3 install dxpy
dxlogin
```

## Running a Workflow

* Create a project on DNAnexus where the workflow and associated files will be stored.
* Once your project has been setup, import the WDL workflow `02_download_collection_files.wdl` to the DNAnexus platform using dxCompiler.

```shell
java -jar ./dxCompiler.jar compile ./examples/wdl/02_download_collection_files.wdl n -project dnastack-client-library-worked-examples n -folder /download_collection_files
```

To run the newly created workflow on the DNAnexus platform, select the project folder and Workflow item, and click "Run" as Analysis.

* To view the progress of the workflow at any time, select the "Monitor" tab.
* Inputs or parameters of the workflow can be modified. For example, to download from a different collection.
* The output files can be found in and downloaded from the folder specified in the Run dialog. In this case, the root of the DNAnexus project.


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