rfplasmid in a docker container errors during rfplasmid --initialize

[juliofdiaz]

Hello,

I am trying to wrap RFPlasmid in a docker container, and I am installing it using conda. When I run the installation step, everything seems to run well. Then I run rfplasmid --initialize as instructed, and it goes well, but docker build exits at that step with an error. Thus the container cannot be built.

I looked into the rfplasmid code and it seems to exit 1 even when the download completed without an error. I found the location of the code to rfplasmid by doing which rfplasmid

    FILE="$rfplasmidpath"/plasmiddb_cge.dmnd
    if [ -f "$FILE" ]; then
        echo
    else
        echo "Error: $FILE does not exist. Run rfplasmid --initialize to download databases"
        exit 1
    fi

    FILE2="$rfplasmidpath"/plasmiddb_total.dmnd
    if [ -f "$FILE2" ]; then
        echo
    else
        echo "Error: $FILE2 does not exist. Run rfplasmid --initialize to download databases"
        exit 1
    fi

why is the exit 1 necessary? Thanks!

[aldertzomer]

if the file plasmiddb_total.dmnd is not downloaded/created using diamond makedb , the script will fail and will exit 1. Where do you see that it will exit 1 when the file is there?