How to specify path to file "sequenceserver.conf" when spawning a docker container from "wurmlab/sequenceserver" image.

sequenceserver
#1

Good afternoon Anurag Priyam,

Thank you for your wonderful blast web application and docker image (“wurmlab/sequenceserver”).

I have successfully run a docker container from the above docker image.
I was wondering if there is a command line argument by which I could set the path to the “sequenceserver.conf” when starting the docker container using docker run command.

Regards,
Allan Kamau.

#2

Hi Allan,

Here’s how:

docker run --rm -itp 4567:4567 -v ~/db:/db -v ~/.sequenceserver.conf:/root/.sequenceserver.conf wurmlab/sequenceserver

Note the second -v argument in the above command. It mounts the configuration file from host to a path in Docker container where sequenceserver reads its configuration from.

However, you would have to be careful to keep the :bin: setting the same, which specifies the path to BLAST+ binaries. Take a look at the configuration file in the docker container:

docker run --rm -itp 4567:4567 -v ~/db:/db -v ~/.sequenceserver.conf:/sequenceserver.conf wurmlab/sequenceserver cat /root/.sequenceserver.conf

(Here, the :database_dir: setting in the configuration file does not matter because it is superseded by the -d option in the CMD line in Dockerfile).

Priyam