Merlin Server

The merlin server command allows users easy access to containerized broker and results servers for merlin workflows. This allows users to run merlin without a dedicated external server.

The main configuration will be stored in the subdirectory called “server/” by default in the main merlin configuration “~/.merlin”. However different server images can be created for different use cases or studies just by simplying creating a new directory to store local configuration files for merlin server instances.

Below is an example of how merlin server can be utilized.

First create and navigate into a directory to store your local merlin configuration for a specific use case or study.

mkdir study1/
cd study1/

Afterwards you can instantiate merlin server in this directory by running

merlin server init

A main server configuration will be created in the ~/.merlin/server and a local configuration will be created in a subdirectory called “merlin_server/”

We should expect the following files in each directory

~/study1$ ls ~/.merlin/server/
docker.yaml  merlin_server.yaml  podman.yaml  singularity.yaml

~/study1$ ls

~/study1$ ls merlin_server/
redis.conf  redis_latest.sif

The main configuration in “~/.merlin/server” deals with defaults and technical commands that might be used for setting up the merlin server local configuration and its containers. Each container has their own configuration file to allow users to be able to switch between different containerized services freely.

The local configuration “merlin_server” folder contains configuration files specific to a certain use case or run. In the case above you can see that we have a redis singularity container called “redis_latest.sif” with the redis configuration file called “redis.conf”. This redis configuration will allow the user to configurate redis to their specified needs without have to manage or edit the redis container. When the server is run this configuration will be dynamically read, so settings can be changed between runs if needed.

Once the merlin server has been initialized in the local directory the user will be allowed to run other merlin server commands such as “run, status, stop” to interact with the merlin server. A detailed list of commands can be found in the Merlin Server Commands page.

Note: Running “merlin server init” again will NOT override any exisiting configuration that the users might have set or edited. By running this command again any missing files will be created for the users with exisiting defaults. HOWEVER it is highly advised that users back up their configuration in case an error occurs where configuration files are overriden.