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statgen / fivex

Interactive eQTL visualizations
MIT License
13 stars 3 forks source link

Set up a development/ staging version of the app #3

Closed abought closed 5 years ago

abought commented 5 years ago

Purpose

We would like to facilitate discussion by creating a web-accessible version. This means getting the app working on a running server.

This ticket is partially blocked by #2, but we can start by identifying a server with the resources required to run the app. This could be a new VM, or reusing an existing machine such as PheWeb's host.

System requirements

I have copied relevant info from a Slack discussion with Alan:

Questions for the chosen environment: Q: How much storage space will the app require for critical data files? A: ...the tabixable data... is currently 191 GB

Q: Are there any privacy/security considerations? A: The GTEx data either is, or will be, publicly available and contains no individual-level data on genotypes or expression, so there should be no problems with privacy or security

Q: Aside from python/flask, are there any key system dependencies? A: [no] other system dependencies .... at the moment, unless it is for some additional functionality that we haven't implemented yet

Notes

The full-size dataset required to run the app may be found on the cluster: /net/amd/amkwong/browseQTL/all_chr/data/add.symbol.column/

abought commented 5 years ago

Peter has set one up on the new PheWeb machine here: https://pheweb.sph.umich.edu/pheget

The documentation still needs to be improved, so I'll tag this documentation but keep it open for now.