Installation Software and References

The following information provides the requirements and steps to install the DRAGEN ORA Helper Suite Software.

Installation Requirements

The following table lists the minimum requirements for the DRAGEN ORA Helper Suite Software.

Component	Minimum Requirement
System memory	8 GB RAM
Free disk space	From 2 GB to 15 GB depending on how many different specific references are needed for the decompression. Specific references are available for downloads in the ORA Support Site. For human data, 2 GB are required. The default human reference is already pre-installed within the Software and does not need to be downloaded.
Compatible Linux distributions	CentOS 7 or later Ubuntu 14 or later Oracle 8 or later
Internet connection	An internet connection is required to install the DRAGEN ORA Helper Suite. Once installed, the internet connection is not required unless the DRAGEN ORA Helper Suite is used in a remote environment.

Info The oraFuse software uses a FUSE file system. Because the FUSE file system requires root privileges, the oraFuse software requires root privileges during installation.

Install the DRAGEN ORA Helper Suite Software

Download the installer from the ORA Support Site, and follow the installation steps below to install the DRAGEN ORA Helper Suite Software. Installation Steps:

1. Open a terminal window.

2. If the installation is for an online system, then move the installer to the directory where the software should be installed. If the installation is for an offline system, then the installer does not need to be moved.

3. Navigate to the installer location.

4. Run the following command:

sh <file name>.sh

5. To install oraFuse, install the dependencies when prompted. The following dependencies will automatically be installed on an online system:

Distribution	Dependencies
CentOS	fuse fuse-libs libcurl openssl
Ubuntu	fuse openssl libcurl3-gnutls
Oracle	fuse fuse-libs fuse-devel libcurl

Info If the installation is for an offline system, then make sure the dependencies are installed on the offline system.

The installer creates a folder named oraHelperSuite. If the installation is for an offline system, then move the oraHelperSuite folder to the offline system. The oraHelperSuite folder contains the following:

• orad executable

• oraFuse executable

• ora-ldpreload.so library

• oraHelper wrapper executable

• the human reference genome used to decompress: refbin. The pre-installed refbin is the default human reference. If the FASTQ.ORA file has been compressed with a different reference ensure the correct reference is available locally or download it from the ORA Support Site.

Install the DRAGEN ORA Decompression References

For decompression of FATSQ.ORA derived from specific species/models, the specific reference needs to be downloaded from the ORA Support Site. The whole reference database can also be downloaded.

Info For default human reference, there is no need to add this extra step. The default human reference is already included in the DRAGEN ORA Decompression Software.

Extract a specific reference

1. Move the downloaded archive to the oraHelperSuite directory

mv yourdownloadpath/<genus_specificname>.tar.gz yourpath/oraHelperSuite

2. Navigate to the oraHelperSuite directory

cd yourpath/oraHelperSuite

3. Extract the archive file using the following command:

tar -xzvf <genus_specificname>.tar.gz (Linux)
tar -xzvf <genus_specificname>.tar.gz (Mac)

When the extraction of the specific reference is completed the oraHelperSuite folder on a linux environment should be structured as follows with example on gallus_gallus reference:

oraHelperSuite   |__orad   |__orafuse   |__ora-ldpreload.so   |__oraHelper   |__refbin   |__Gallus_gallus        |__refbin        |__readme_gallus_gallus

Extract the full database

1. Move the downloaded archive to the oraHelperSuite directory

mv yourdownloadpath/oradata.tar.gz yourpath/oraHelperSuite

2. Navigate to the the oraHelperSuite directory

cd yourpath/oraHelperSuite

3. Extract the archive file using the following command:

tar -xzvf oradata.tar.gz (Linux)
tar -xzvf oradata.tar.gz (Mac)

When the extraction of the full database is completed the the oraHelperSuite folder on a linux environment should be structured as follows:

oraHelperSuite   |__orad   |__orafuse   |__ora-ldpreload.so   |__oraHelper   |__refbin   |__oradata     |__Homo_sapiens       |__refbin       |__readme_homo_sapiens     |__Homo_sapiens_bisulfite       |__refbin       |__readme_homo_sapiens_bisulfite     |__Genus_specificname       |__refbin        |__readme_Genus_specificname