Not able to run docker container with mount

Hello,

I am trying to write a python program to run a third party docker image using docker-py. Unfortunately, I am not able to run the third-party program successfully.

I am trying to implement the program using the following:

• Python 3.6
• docker==5.0.3

Following is the docker command I am trying to mimic with docker-py:

docker run --rm --user root -v /host/dir:/container_dir quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0 /bin/bash -c "variant_recoder --input_file /container_dir/test_input.txt --pretty --species homo_sapiens > /container_dir/test_output.json"

import docker

client = docker.from_env()

working_dir = "/home/user/downloads/"
container_dir = "/data"
input_file = "test_input.txt"
output_file = "tes_toutput.json"

container = client.containers.run(image="quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0",
                            command=["variant_recoder", "--input_file", input_file, "--pretty", "--species", "homo_sapiens", ">", output_file],
                            volumes={working_dir: {"bind":container_dir, "mode": "rw"}},
                            user="root",
                            remove=True
                           )
print(container)

Following is the error I am experiencing when running the above python script. I believe the mounting of the directory is not happening and because of that, the program is not able to read the file.

Error log:

docker.errors.ContainerError: Command '['variant_recoder', '--input_file', '/data/test_vep_test_input.txt', '--pretty', '--species', 'homo_sapiens', '>', '/data/docker_vep_recoder_output.json']' in image 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' returned non-zero exit status 2: b'Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.\n\n-------------------- EXCEPTION --------------------\nMSG: ERROR: File "/data/test_vep_test_input.txt" does not exist\n\nSTACK Bio::EnsEMBL::VEP::Parser::file /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/Parser.pm:231\nSTACK Bio::EnsEMBL::VEP::Parser::new /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/Parser.pm:125\nSTACK Bio::EnsEMBL::VEP::Runner::get_Parser /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm:801\nSTACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm:828\nSTACK Bio::EnsEMBL::VEP::Runner::init /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm:136\nSTACK Bio::EnsEMBL::VEP::VariantRecoder::init /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/VariantRecoder.pm:160\nSTACK Bio::EnsEMBL::VEP::VariantRecoder::recode_all /usr/local/share/ensembl-vep-104.3-0/modules/Bio/EnsEMBL/VEP/VariantRecoder.pm:182\nSTACK main::main /usr/local/bin/variant_recoder:104\nSTACK toplevel /usr/local/bin/variant_recoder:97\nDate (localtime)    = Wed Nov 17 21:17:41 2021\nEnsembl API version = 104\n---------------------------------------------------\n'

If anyone can point out what am I doing wrong, I would greatly appreciate the help.

Thank you.

Start at client.containers.run and compare its command and volumes arguments with the documented docker-py behavior for the equivalent Docker command. Reproduce the reported container invocation and determine whether the failure comes from mounting the host path or from passing shell redirection as a command argument; done means identifying a confirmed library issue or documenting the correct invocation.