Docker-based deployment of the full MedCo stack.
Diffusion MedCo Deployment (riccardo)
Recent Commits
Recent Commits
Commit | Author | Details | Committed | ||||
---|---|---|---|---|---|---|---|
1b56d168d728 | sacchi | merge conficlts | Jul 6 2018 | ||||
e6b5bd231f48 | sacchi | add step to README | Jul 6 2018 | ||||
38be675e5212 | root | README | Jul 6 2018 | ||||
9288ac887645 | sacchi | add README | Jul 6 2018 | ||||
e5dc22a64bb4 | root | web client branch | Jul 6 2018 | ||||
c389d5badd13 | root | Merge branch 'riccardo' of https://c4science.ch/source/medco-deployment into… | Jul 3 2018 | ||||
b7b324cf74b0 | root | dockerfile | Jul 3 2018 | ||||
9de956a8a8ce | root | removed test3 | Jul 3 2018 | ||||
a4eff6adf334 | root | merge | Jul 3 2018 | ||||
449f518efee5 | root | medco databases | Jul 3 2018 | ||||
b79246408293 | root | fix docker compose common | May 3 2018 | ||||
d499d5f7c914 | root | restore network compose common | May 3 2018 | ||||
f40019b53ac3 | root | 3/6/9/10 configurations 03/05/18 | May 3 2018 | ||||
fca98c8f4a56 | mickmis | change to genomic annotations format | Apr 29 2018 | ||||
c678c56a73c6 | mickmis | remove some things to fit the new loader | Apr 28 2018 |
README.md
README.md
- Deployment
- Clone riccardo branch of medco-deployment in the three servers and install dependencies.
`sh
$ cd ~
$ git clone https://c4science.ch/source/medco-deployment.git
$ git checkout riccardo
$ bash ~/medco-deployment/resources/utility-scripts/ubuntu_prereqs_setup.sh
`
Notice that:
- in medco-deployment/docker-images/i2b2-database/Dockerfile we added the following commands to allow TCP/IP connection and avoid an error during the data loading phase. `
- hack postgresql docker image to allow transmart loading (allow TCP/IP connections during init phase) RUN sed -i "s/listen_addresses=''/listen_addresses='*'/g" /usr/local/bin/docker-entrypoint.sh `
- medco-deployment/docker-images/i2b2-web/Dockerfile is set to swith to the fork/1.22.8-medco_dev branch of the shrine webclient. ` SHRINE_VERSION="fork/1.22.8-medco_dev" `
- Follow the steps described in the section Deploying MedCo on Different Servers \(For Development\) to create the CA certificate and also to build and run the dockers.
- Copy the generated group.toml to shrine-webclient/src/main/html/js-i2b2/cells/plugins/MedCo/gropu.toml (and push it on fork/1.22.8-medco_dev branch) so that the webclient can use it to compute the aggregate key.
- Load the databases by executing the following script from only one server: ` sh $ ./loadData-3nodes-iccluster.sh ` Ask Joao for details of where to find this script.
ATTENTION: if the log file of the i2b2-server container returns an "insufficient permissions" error for table i2b2medco.medco_project_user_budget or i2b2medco.medco_hash_noise after a query is performed, manually grant all the privileges for the users "i2b2medco" and "postgres" in both tables.
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