# Quick Start

## Quick Start Guide

### Table 1. Release Information

| Execution Environment | software version                                                                       | Client program                   | location       | Note                                                                                                                      |
| --------------------- | -------------------------------------------------------------------------------------- | -------------------------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------- |
| Local Dragen Server   | 4.4.4.62                                                                               | run\_Heme\_WGS\_TO\_{version}.sh | /usr/local/bin | See [Dragen Server](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation/launching-analysis.md) |
| ICA                   | a11697ba-1144-4dc6-9e22-f21dff29f747                                                   | icav2                            | ICA Pipelines  | See [ICA Cloud](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup.md)                               |
| ICA                   | urn:ilmn:ica:pipeline:a11697ba-1144-4dc6-9e22-f21dff29f747#Heme\_WGS\_TO\_v4\_4\_4\_62 | supported browser                | ICA UI         | See [ICA Cloud](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/launching-analysis.md)            |

* {version} is used to represent the software version number in Table 1 above. Similarly, `<pipeline_run_script>` is used to indicate the client program name in this document.

#### Download, Install and Execute on a Local Server

The software may be [downloaded](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation.md#downloader) and installed by following the [installation guide](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/installation.md#installation-instructions). It may be executed using a local DRAGEN server or on a local computer which launches the analysis in the ICA cloud environment.

#### Run analysis on a local DRAGEN Server

The command line program may be used to launch an analysis by using the `<pipeline_run_script>` with the appropriate options.

**start from bcl**

```bash
<pipeline_run_script> --help # list all supported parameters
<pipeline_run_script> --inputType bcl \
--inputFolder /staging/input-folder \
--analysisFolder /staging/output-folder
```

**start from one or more input folders when using FASTQ, BAM or CRAM files**

Multiple folders may be specified as input folders in comma separated values when using FASTQ, BAM or CRAM files as input.

```bash
<pipeline_run_script> --inputType <fastq|bam|cram> \
--inputFolder /staging/input-folder-1,/staging/input-folder-2 \
--analysisFolder /staging/output-folder
```

Pressing Ctrl+C during a DRAGEN step stops the currently running analysis and might cause an FPGA error. To recover from an FPGA error, shut down and restart the server.

#### Run analysis on ICA using the icav2 client

Here is an example of starting an analysis using the ICA client by providing the necessary command parameters and specify a particuar storage size for analysis in ICA.

```sh
icav2 projectpipelines start nextflow ${PIPELINE_ID} \
--project-id ${ANY_PROJECT_ID} \
--storage-size Large \
-o json \
--input ${ANY_SAMPLE_SHEET} \
--input ${ANY_INPUT_DIR} \
--parameters inputType:'bcl' \
--parameters referenceGenome:'hg38' \
--parameters oraCompressionEnabled:'true' \
--parameters sampleIds:'1267-Prostate-Del-R1,741-Lung-SNV-R1' \
--user-reference ${ANY_USER_REFERENCE}
```

### Run analysis on ICA using UI

The same analysis example above may be completed using the ICA UI by logging into the appropriate domain of your company and project where the Heme pipeline is [set up](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup.md).

Find more information in the [ICA Cloud App Launch Guide](/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/launching-analysis.md).

## Turn Around Time Comparison

### ICA

Coming soon.

### Local Server

#### Local Server Only

Coming soon.

#### Data Streaming from NFS

Coming soon.


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