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config/fractalis Release of new beta version (18.1-beta-17) Dec 6, 2018
.env preparing for quickstart release 18.1(not beta) Dec 16, 2018
Dockerfile-fractalis hotfix for LCSB-BioCore/Fractalis#4 Dec 14, 2018
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README.md Update README.md Dec 16, 2018
ReleaseNotes-18.1-beta-17.md
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README.md

i2b2/tranSMART release-18.1 Quick-Start, and PIC-SURE HPDS UI

Database is pre-populated with the CDC NHANES public dataset (41,474 patients with 1,300 variables per patient)

Docker Host Hardware Requirements

Docker Network Requirements

  • HTTP (80) and HTTPS (443) ports (default)
  • Edit .env file to assign different ports
HTTP_PORT=
HTTPS_PORT=

Compatible Docker Versions

Docker: 17.06.2+
docker-compose: 1.21.0+

Deploy

Note: If you have already installed an older version of the Quickstart you must stop it before starting the new one. The best approach is to recreate your docker-machine from scratch.

start by running the new PIC-SURE HPDS UI, it will give you something to do while the other images download.

$ docker-compose up -d nhaneshpds

The i2b2/tranSMART images will take several minutes to become available, while you wait you should check out the new PIC-SURE HPDS UI which will be the landing page of your stack. Browse to your docker-machine IP to try it out as you wait for the remaining steps of the setup to complete. You will still need to check on each of the following steps as they will run into intermittent network failures while you download about 40GB of compressed data. To get to i2b2/tranSMART once the following steps have completed successfully, click the Advanced Phenotype Search button in the PIC-SURE UI.

Note: when you run this next command it will download about 40GB of data from the internet. Please be mindful of this if you are charged for data transfer.

images take several minutes to download, start by just downloading the DB image

$ docker-compose pull db

NOTE: if you are running docker-compose version 1.21.0+ and the pull command fails, try:

$ docker-compose pull --no-parallel db

deploy database first deploy only

database may hang here for a few minutes

$ export COMPOSE_HTTP_TIMEOUT=300
$ docker-compose up -d db

download all other images while the DB starts up

$ docker-compose pull

deploy i2b2/tranSMART + fractalis

$ docker-compose up -d

To stop and remove the stack

# -v will remove any associated persistent volumes, including the database, with the stack
$ docker-compose down -v

Test i2b2/tranSMART release-18.1

  1. Browse to your docker machine IP and click the Advanced Phenotype Search link.

Troubleshoot

If you get "socket read timeout" errors while pulling the images, just retry the pull. Eventually it will succeed.

Biggest point of failure is deploying the database for the first time. Due to its size and resource requirements, your Docker client may timeout during first deployment of the database.

Open discussion forum

https://discuss.i2b2transmart.org

Docker-machine installation - MAC/Windows

https://tinyurl.com/docker-VM <- These are the unofficial instructions created for i2b2/tranSMART, they are probably out of date, use the official ones instead : https://docs.docker.com/machine/install-machine/

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