misolims/miso-lims-webapp repository overview

⁠Available Tags

• latest Dockerfile⁠

Check the Tags⁠ page for the latest versions.

Older, unsupported versions of MISO in a single standalone container are available at misolims/miso-lims⁠

⁠Quick reference

• Getting started:
  • Plain sample Walk-throughs⁠
  • Detailed sample Walk-throughs⁠
• User Manual⁠
• Where to get help: Gitter⁠
• Where to file issues: Github issue tracker⁠

⁠What is MISO?

MISO (Managing Information for Sequencing Operations) is an open-source Laboratory Information Management System (LIMS) specifically designed for tracking next-generation sequencing experiments.

Sequencing centres differ not only in terms of their scale and output, but also their requirements for information management. Sequencing platforms are becoming more accessible, and the efficient storage of genomic metadata is vital for large and small sequencing centres alike. Off-the-shelf solutions are often very expensive and not cost-effective for the smaller centre. Furthermore, support contracts are often required, and the extensibility of these systems is not in the hands of the metadata generators. In terms of implementation, as well as the desire to tailor an information system in-house, data formats can change and platforms can evolve rapidly. These are valid concerns for both large centres characterised by high-throughout data production and smaller scale laboratories with constrained expenditure for IT solutions, and potentially project specific metadata requirements.

For more information, a full manual and user guides, see the MISO website⁠.

⁠How to start MISO

The easiest way to bring up a particular version of MISO (including webapp and database containers) is to launch it using docker-compose. A starting docker-compose.yml⁠ file is available in the miso-lims Github repo⁠

Download the basic docker-compose files.

wget -r https://raw.githubusercontent.com/miso-lims/miso-lims/develop/docker-compose.yml https://raw.githubusercontent.com/miso-lims/miso-lims/develop/docker-compose.override.yml https://raw.githubusercontent.com/miso-lims/miso-lims/develop/docker-compose.detailed.yml https://raw.githubusercontent.com/miso-lims/miso-lims/develop/.docker

Set required environment variables and set the password for the database

export MISO_DB_USER=tgaclims MISO_DB=lims MISO_DB_PASSWORD_FILE=./.miso_db_password MISO_TAG=latest
echo "changeme" > ./.miso_db_password

Bring up the environment. By default this will use docker-compose.yml and docker-compose.override.yml.

docker-compose up

⁠How to use miso-lims-webapp

⁠How to start the standalone webapp

To use the webapp container with defaults, start it:

docker-compose up

The webapp depends on a connection to a MISO MySQL database that has been migrated using the miso-lims-migration⁠ container.

This connection is configured by passing environment variables to the container:

• MISO_DB_HOST_PORT : the hostname and the port to connect to. The hostname can either be a full DNS name, without the protocol e.g. myserver.mycompany.com, or refer to a link to another container. (default: 'db:3306')
• MISO_DB_PASS_FILE : a file with a single line containing the password for the MYSQL user used to query and update the DB. This can be the path to a docker secret (default: /run/secrets/lims_password)
• MISO_DB : the name of the MISO db on the indicated host (default: 'lims')
• MISO_DB_USER : the MySQL user on the host DB (default: tgaclims)