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miso-lims-develop (0, 2023-09-28)
miso-lims-develop\.docker (0, 2023-09-28)
miso-lims-develop\.docker\demo.detailed.yml (3158, 2023-09-28)
miso-lims-develop\.docker\demo.plain.yml (2574, 2023-09-28)
miso-lims-develop\.docker\detailed_sample_config (0, 2023-09-28)
miso-lims-develop\.docker\detailed_sample_config\V0792__drop-inconvenient-rows.sql (323, 2023-09-28)
miso-lims-develop\.docker\detailed_sample_config\V0793__detailed_sample_data.sql (20404, 2023-09-28)
miso-lims-develop\.docker\detailed_sample_config\miso.properties (3634, 2023-09-28)
miso-lims-develop\.docker\nginx (0, 2023-09-28)
miso-lims-develop\.docker\nginx\http.conf (451, 2023-09-28)
miso-lims-develop\.docker\nginx\self-sign-cert.sh (464, 2023-09-28)
miso-lims-develop\.docker\nginx\ssl.conf (721, 2023-09-28)
miso-lims-develop\.docker\run-flyway (1172, 2023-09-28)
miso-lims-develop\.docker\tomcat (0, 2023-09-28)
miso-lims-develop\.docker\tomcat\ROOT.xml (887, 2023-09-28)
miso-lims-develop\.docker\tomcat\logging.properties (2379, 2023-09-28)
miso-lims-develop\.docker\tomcat\setenv.sh (255, 2023-09-28)
miso-lims-develop\.dockerignore (163, 2023-09-28)
miso-lims-develop\.env (176, 2023-09-28)
miso-lims-develop\.mkdocs.yml (2876, 2023-09-28)
miso-lims-develop\.prettierrc.json (430, 2023-09-28)
miso-lims-develop\.readthedocs.yml (311, 2023-09-28)
miso-lims-develop\.vscode (0, 2023-09-28)
miso-lims-develop\.vscode\eclipse-java-google-style.xml (36004, 2023-09-28)
miso-lims-develop\.vscode\extensions.json (471, 2023-09-28)
miso-lims-develop\.vscode\launch.json (402, 2023-09-28)
miso-lims-develop\.vscode\settings.json (591, 2023-09-28)
miso-lims-develop\CONTRIBUTING.md (3387, 2023-09-28)
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      [](https://zenodo.org/badge/latestdoi/472***28) [](https://gitter.im/miso-lims/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [](https://miso-lims.readthedocs.io/projects/docs/en/latest/?badge=latest) # MISO: An open source LIMS for small-to-large scale sequencing centres © 2019. [Ontario Institute for Cancer Research](http://oicr.on.ca), Toronto, Canada, [Earlham Institute](http://earlham.ac.uk/), Norwich, UK. > MISO project contacts: [Morgan Taschuk](morgan.taschuk@oicr.on.ca), [Robert Davey](robert.davey@earlham.ac.uk) > > 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 . ## Trying MISO ### Docker The simplest way to get MISO up and running quickly is to use [Docker](https://www.docker.com/) compose. Images of the most recent MISO releases are available on Docker Hub in the [misolims](https://hub.docker.com/r/misolims/) organisation. #### Prerequisites Install required dependencies: 1. [Install Docker 18.06.0+](https://docs.docker.com/install/) 1. If necessary, [install Docker Compose](https://docs.docker.com/compose/install/) 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 -> Library Aliquot -> Pool workflow and is sufficient for basic laboratory tracking for sequencing. Launch the plain sample demo with docker-compose: ``` bash 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: ```bash 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.detailed.yml up ``` For both environments, navigate to [http://localhost](http://localhost) and use the credentials **admin**/**admin**. Once you are finished with the container, make sure to run `docker-compose -f down`, where `` 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](https://miso-lims.readthedocs.io/projects/docs/en/latest/admin/compose-installation-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](https://miso-lims.github.io/walkthroughs/index-plain) * [Detailed sample tutorials](https://miso-lims.github.io/walkthroughs) Some of the resources (MISO URL, ways of contacting the MISO administrators) can be changed by forking and configuring the [tutorial repository](https://github.com/miso-lims/walkthroughs) 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](https://github.com/miso-lims/miso-lims/releases/latest). Installation and configuration details can be found in the [MISO building and deploying guide](https://miso-lims.readthedocs.io/projects/docs/en/latest/admin/installation-guide/). ## Contact and Community - [MISO Twitter](https://twitter.com/misolims) : for news and updates - [MISO Community Gitter](https://gitter.im/miso-lims/community) : for user group and developer questions and discussion - [MISO Users Gitter](https://gitter.im/miso-lims/users) : for user group questions and discussion - [MISO Developers Gitter](https://gitter.im/miso-lims/developers) : for developer questions and discussion

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