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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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Difficulty using AmpliconArchitect docker on google cloud platform #75

Open riazgillani opened 3 years ago

riazgillani commented 3 years ago

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.

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 commented 3 years ago

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.