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

Hi, there

I referred to the article below.


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.

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 https://www.nvidia.com/en-us/docs/nvidia-parabricks-general/

Regards,
Myrieme

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.)