inkimar / miso-lims

MISO: An open-source LIMS for NGS sequencing centres

MISO: An open source LIMS for small-to-large scale sequencing centres

© 2017. Earlham Institute, Norwich, UK, Ontario Institute for Cancer Research, Toronto, Canada

MISO project contacts: Robert Davey, Morgan Taschuk

MISO is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

MISO is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with MISO. If not, see http://www.gnu.org/licenses/.

Trying MISO

Docker

The simplest way to get MISO up and running quickly is to use Docker compose. Images of the most recent MISO releases are available on Docker Hub in the misolims organisation.

Prerequisites

Install required dependencies:

1. Install Docker 18.06.0+
2. If necessary, install Docker Compose

Download and extract the .docker directory from Github into miso-lims-compose.

wget https://github.com/miso-lims/miso-lims/archive/master.zip
unzip master.zip 'miso-lims-master/.docker/*'
mv miso-lims-master/.docker miso-lims-compose
rm -r master.zip miso-lims-master/

You are now ready to run MISO.

Quick Start

To bring up a demo environment, install the pre-requisites above and run the following commands.

Plain sample mode has a straightforward Sample -> Library -> Dilution -> Pool workflow and is sufficient for basic laboratory tracking for sequencing.

Launch the plain sample demo with docker-compose:

cd miso-lims-compose
export MISO_DB_USER=tgaclims && export MISO_DB=lims && export MISO_DB_PASSWORD_FILE=./.miso_db_password && export MISO_TAG=latest
echo "changeme" > ./.miso_db_password
docker-compose -f demo.plain.yml up

Detailed sample mode has all of the features of plain sample mode, plus it allows users to build a hierarchy of Samples (e.g. Identity -> Tissue -> Slide -> gDNA (stock) -> gDNA (aliquot) and also includes alias autogeneration.

Launch the detailed sample demo with docker-compose:

cd miso-lims-compose
export MISO_DB_USER=tgaclims && export MISO_DB=lims && export MISO_DB_PASSWORD_FILE=./.miso_db_password && MISO_TAG=latest
echo "changeme" > ./.miso_db_password
docker-compose -f demo.detailed.yml up

For both environments, navigate to http://localhost and use the credentials admin/admin.

Once you are finished with the container, make sure to run docker-compose -f <compose.yml> down, where <compose.yml> is either demo.plain.yml or demo.detailed.yml. This will clean up the instances and networks and release their resources to the host operating system.

These compose files are intended as a demonstration and not a permanent installation.

Please see the Docker Compose Guide for more information on configuring the containers and the compose files.

User Tutorial

There are tutorials available to introduce and train new users to MISO's functionality.

• Plain sample tutorials
• Detailed sample tutorials

Some of the resources (MISO URL, ways of contacting the MISO administrators) can be changed by forking and configuring the tutorial repository to suit your lab's specific needs.

Running an Instance of MISO

To run your own MISO instance in the long term, download the latest release.

Installation and configuration details can be found in the MISO installation guide.

Contact and Community

• MISO Twitter : for news and updates
• MISO Community Gitter : for user group and developer questions and discussion
• MISO Users Gitter : for user group questions and discussion
• MISO Developers Gitter : for developer questions and discussion
• Slack Group : for developers