Difficulty using AmpliconArchitect docker on google cloud platform

[riazgillani]

Hello,

I am trying to utilize the AmpliconArchitect docker image for a workflow in an instance of the google cloud platform. In my workflow, I have written the following based on what I saw in the structure of the docker when I ran it in interactive mode (with bam_file, bed_file, and sample_name being inputs into my workflow):

<<< cd /home

bash /programs/AmpliconArchitect-master/docker/run_aa_docker.sh --bam ${bam_file} --bed ${bed_file} --out ${sample_name}

However, I receive the following error when I run my workflow: "/programs/AmpliconArchitect-master/docker/run_aa_docker.sh: No such file or directory"

I am having a hard time understanding this error, as I thought this was a valid path based on what I understood of the docker structure.

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Separately, I have also tried utilizing docker on my local machine. However, when executing the Bash script run_aa_docker.sh, I receive the following error "docker: Error response from daemon: create .: volume name is too short, names should be at least two alphanumeric characters."

Looking at the .sh script, I thought this could be because AA_DATA_REPO, BAM_DIR, BED_DIR, OUT_DIR, or MOSEKLM_LICENSE_FILE are incorrectly defined. I have set AA_DATA_REPO=/Users/riazgillani/data_repo and MOSEKLM_LICENSE_FILE=/Users/riazgillani/mosek/mosek.lic in my .bashrc file (and sourced it). And if I understand the shell script correctly, BAM_DIR, BED_DIR, and OUT_DIR should be set by the inputs I have provided to the .sh script (of note, the BAM and BED files live on the cloud, and I have provided links to these files after appropriate authentication on my local machine).

If you have any advice navigating the use of the docker image as part of a workflow on the google cloud platform or locally, I'd really appreciate it!

Thanks, Riaz

[virajbdeshpande]

Hello @riazgillani , Apologies for the slow reply, I am not sure why it is reporting this error. I will look into this and reply back in about a week.