[Nvidia/Parabricks] What is the correct path of license.bin in a container?

Healthcare Parabricks
1

Hi, there

I referred to the article below.
https://ngc.nvidia.com/catalog/containers/hpc:parabricks
And ran the pbrun tools via docker.

When I executed the fq2bam tool, the log shows that
“The license file license.bin was not found in the installation folder”

$ docker run --rm -v /home/anonymous/software/parabricks/license.bin:/opt/parabricks/license.bin   -v /home/anonymous/parabricks/dataset/D99999_S99_L001/:/dataset/ nvcr.io/hpc/parabricks:v2.5.0 fq2bam   --ref /dataset/human_g1000_v37_decoy.fasta   --in-fq /dataset/D99999_S99_L001_R1.fastq.gz /dataset/D99999_S99_L001_R2.fastq.gz   --out-bam /dataset/out.bam
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /dataset/D99999_S99_L001_R1.fastq.gz and
/dataset/D99999_S99_L001_R2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1
License file license.bin not found in installation folder or passed in as argument
Please contact support@parabricks.com for any questions. Exiting...

I tried to solve this case in different ways, but all failed…

including putting the license.bin in

  • /opt/parabricks/license.bin
  • /parabricks/license.bin
  • /usr/local/nvidia/bin/license.bin
  • /usr/local/cuda/bin/license.bin
  • /dataset/license.bin

And, the following config was from the container I executed.
$docker inspect container_id

"Mounts": [
    {
        "Type": "bind",
        "Source": "/home/anonymous/software/parabricks/license.bin",
        "Destination": "/parabricks/license.bin",
        "Mode": "",
        "RW": true,
        "Propagation": "rprivate"
    },
    {
        "Type": "bind",
        "Source": "/home/anonymous/parabricks/dataset/D99999_S99_L001",
        "Destination": "/dataset",
        "Mode": "",
        "RW": true,
        "Propagation": "rprivate"
    }
],
"Config": {
    "Hostname": "a2c2b59ded40",
    "Domainname": "",
    "User": "",
    "AttachStdin": false,
    "AttachStdout": true,
    "AttachStderr": true,
    "Tty": false,
    "OpenStdin": false,
    "StdinOnce": false,
    "Env": [
        "PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
        "CUDA_VERSION=9.0.176",
        "CUDA_PKG_VERSION=9-0=9.0.176-1",
        "LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64",
        "NVIDIA_VISIBLE_DEVICES=all",
        "NVIDIA_DRIVER_CAPABILITIES=compute,utility",
        "NVIDIA_REQUIRE_CUDA=cuda>=9.0",
        "ENV=~/.profile"
    ],
    "Cmd": [
        "fq2bam",
        "--ref",
        "/dataset/human_g1000_v37_decoy.fasta",
        "--in-fq",
        "/dataset/D99999_S99_L001_R1.fastq.gz",
        "/dataset/D99999_S99_L001_R2.fastq.gz",
        "--out-bam",
        "/dataset/out.bam"
    ],
    "Image": "nvcr.io/hpc/parabricks:v2.5.0",
    "Volumes": null,
    "WorkingDir": "",
    "Entrypoint": [
        "/parabricks/run_pipeline.py"
    ],
    "OnBuild": null,
    "Labels": {
        "com.nvidia.cuda.version": "9.0.176",
        "com.nvidia.volumes.needed": "nvidia_driver",
        "maintainer": "NVIDIA CORPORATION <cudatools@nvidia.com>"
    }
},

Therefore, I would like to know how to configure license.bin in the container in the right way.

2

Hello,

We are sorry you were not able to use our software.

To be able to use Clara Parabricks Pipelines, you need to have access to the installer.

You can get a trial version using this link NVIDIA Clara Parabricks: 90 Day Free Trial

Regards,
Myrieme

3

Yeah, I have got the trial parabricks license key from

But my Question is:

I am not clear about what the differences between A and B are.
Where:


Now, I know that both of them are launched by nvidia-docker.

$ nvidia-docker run \
    --rm \
    -v /opt/parabricks/:/INSTALL/ \
    -v /mnt/parabricks/dataset:/dataset \
    -w=/dataset \
   nvcr.io/hpc/parabricks:v2.5.0 \
   fq2bam \
    --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
    --in-fq parabricks_sample/Data/sample_1.fq.gz parabricks_sample/Data/sample_2.fq.gz \
    --out-bam output.bam \
    --x3

The image can be:

  • nvcr.io/hpc/parabricks:v2.5.0 (version: v2.5.0)
  • parabricks/release:v3.1.1 (version: v3.1.1)

And the key point of license.bin is

# The license.bin should be placed under the /INSTALL/ folder in the container.
-v /opt/parabricks:/INSTALL/

(Please correct me if I’m wrong.)