Commands for the ORA Helper Suite software
oraHelper Interactive User Guide
The oraHelper interactive user guide helps you to determine which of the DRAGEN ORA Helper Suite software to use with your intended downstream bioinformatics software. The oraHelper interactive user guide also displays the correct syntax to use.
Info To get the relevant information about the intended downstream bioinformatics software, the bioinformatics software must be in the PATH variable.
Use the oraHelper interactive user guide as follows:
1. Open a terminal window.
2. Add the oraHelperSuite directory to your PATH as follows:
PATH=<oraHelperSuite Directory>:$PATH
3. Enter oraHelper followed by the intended downstream software command and the input *.fastq.ora file name.
$ oraHelper <command> <file name>.fastq.ora
Examples
The following example shows oraHelper used with the bwa command.
$ oraHelper bwa -i <filename>.fastq.ora
The output will print the proper syntax for each of the DRAGEN ORA Helper Suite software.
The following example shows the output of oraHelper used with the head command.
$ oraHelper head <file name>.fastq.ora
The following example shows the output of oraHelper used with the head command.
Command line Options
| Command | Required | Description |
|---|---|---|
-v --version | No | Print the version of the DRAGEN ORA Helper Suite Software along with the versions of the orad, oraFuse, and ora LD-Preload software. |
oraFuse Software
The oraFuse software requires root privileges during installation. Refer to Installation Requirements.
The oraFuse software creates a virtual FASTQ file for each FASTQ.ORA file in the directory. The virtual file created has a *.fastq file extension instead of a *fastq.gz file extension.
Info Make sure you indicate a *.fastq file extension as input.
Local Environment
1. The oraFuse software runs with the following dependencies: fuse, fuse- libs, libcurl and openssl. If the dependencies were not installed during the DRAGEN ORA Helper Suite Software installation, run the following command.
$ sudo yum install fuse fuse-libs libcurl openssl
2. Add the oraHelperSuite directory to your PATH as follows.
PATH=<oraHelperSuite DIR>:$PATH
3. Enter the following command to mount the oraFuse software to the directory where the FASTQ.ORA files are located.
$ oraFuse
4. Run the desired command on the virtual *.fastq file.
5. When finished, enter the following command to unmount the oraFuse software from the directory.
$ oraFuse --unmount
Examples
The following examples show the results of the oraFuse software with the ls command.
Before oraFuse has been mounted to the current directory:
r10K_1.fastq.ora
After oraFuse has been mounted to the directory:
https: r10K_1.fastq r10K_1.fastq.ora s3:
After oraFuse has been mounted to the current directory with
ls -l:
The following example shows the head command on a virtual FASTQ file after oraFuse has been mounted.
$ head <file name>.fastq
The following example shows the bwa command on a virtual FASTQ file after oraFuse has been mounted.
$ bwa mem -t 8 -M <FASTA> -o <SAM> <file name>.fastq
Remote Environment
The oraFuse software works on FASTQ.ORA files located in AWS s3 or in Azure Blob Storage. The AWS and Azure Blob Storage account configurations and credentials are used for authentication. Refer to Remote and Local Usage section.
The steps to use the oraFuse software in the remote environment are the same as those used in the local environment.
Info Azure Blob is not supported If you are using DRAGEN v3.7 as a downstream software.
The following command shows the remote and virtual files on S3.
$ ls s3 -l s3://bucket/<path>
Examples
The following example runs BWA on S3 files.
$ bwa mem -t 8 -M <FASTA> -o <SAM> s3://bucket/path/<file name>.fastq
When using DRAGEN v3.7 as a downstream software, you can use oraFuse in the remote environment if the location of a file gets passed by specifying the file name as follows:
.virtual/ora/s3:/bucket/<file name>.fastq
The following is an example of using DRAGEN v3.7 on a single FASTQ.ORA located on AWS S3:
Comman Line Options
| Command | Required | Description |
|---|---|---|
--unmount | No | To unmount oraFuse from the directory |
Info Multiple users of the same file are not supported.
Error Messages
If you receive an error message while using the oraFuse software, use the following command to get more information.
$ cat .virtual/ora/.error
ora LD-Preload Software
The ora LD-Preload software creates a virtual FASTQ file for each FASTQ.ORA file in the directory. The virtual file created has a *.fastq file extension instead of a *fastq.gz file extension.
Info Make sure you indicate a *.fastq file extension as input.
Local Environment
1. Add the oraHelperSuite directory to your PATH as follows.
PATH=<oraHelperSuite Directory>:$PATH
2. Run the command with the ora LD- Preload shared library on the *.fastq file as follows.
$ LD_PRELOAD=<oraHelperSuite direcory>/ora-ldpreload.so <command><input file name>.fastq
Examples
The following is an example of the ora LD-Preload software with the 'bwa' command.
$ LD_PRELOAD=<oraHelperSuite DIR>/ora-ldpreload.so bwa mem -t 8 -M <FASTA> -o <SAM> <file name>.fastq
The following is an example of the ora LD-Preload software with the ls command.
$ LD_PRELOAD=<oraHelperSuite DIR>/ora-ldpreload.so ls
The following shows the output of the ora LD-Preload software with the ls command.
<file name>.fastq.ora <file name>.fastq (virtual file)
Remote Environment
The ora LD-Preload software works on FASTQ.ORA files located in AWS s3 or Azure Blob Storage. The software reuses the AWS or Azure Blob Storage account configuration and credentials. Refer to Remote and Local Usage section.
The steps to use the ora LD-Preload software in the remote environment are the same as those used in the local environment. The features are the same, with the following exceptions:
In the remote environment, the ora LD-Preload software does not work on statically compiled bioinformatics software.
In the remote environment, the Linux shell auto-completion feature does not work on virtual files.
orad Software
Orad is the executable of the DRAGEN ORA decompression software. It uses the pipe process, or pipe substitution process, to reduce reads/writes to the disk. If the downstream bioinformatics software do not work with pipes or process substitution, and the oraFuse software or the ora LD-Preload software cannot be used, then fully decompressed temporary files are required. Refer to Troubleshooting section for more information.
The steps are the same for local and remote environments.
Local Environment
1. Add the oraHelperSuite directory to your PATH as follows.
PATH=<oraHelperSuite DIR>:$PATH
2. Enter the command with orad and the pipe or process substitution on the *.fastq.ora files. See the following examples.
Examples
Example with pipe:
When the downstream command or bioinformatics software can read from the standard input, the pipe process is used. The following is an example with the head command. The - c option decompresses to standard output.
$ orad <file name>.fastq.ora -c --raw | head
Example with process substitution:
When the downstream bioinformatics software cannot read from the standard input, for example md5sum, process substitution is used. The following example shows the command with process substitution.
$ md5sum <( orad -c --raw "<file name>.fastq.ora" )
Remote environment
The orad software works on FASTQ.ORA files located in AWS s3 or in Azure Blob Storage. The software reuses the AWS or Azure Blob account configuration and credentials. Refer to Remote and Local Usage section.
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