Trouble setting up the Shiny app and MySQL database about qc4metabolomics HOT 3 CLOSED

Hi,

it is not really in a state where it is easy to get it to run. The plan was to make a docker container, but since I changed jobs it is on hold for the moment.
You would at least need to:

1. Clone the repo properly instead of downloading. When you download the git LFS doesn't work and you therefore don't get the packrat R libraries copied properly.
2. Then you need to start R in the shiny folder and make sure all packages are installing properly
3. AFAIC you need to copy the config file to the root and modify appropriately.
4. Then you need to use init/init_db.R to setup the database properly.
5. Probably something I forgot...

from qc4metabolomics.

Fantastic. I got it working doing the following.

git2r::clone(url = "https://github.com/stanstrup/QC4Metabolomics.git")

library(MetabolomiQCsR)

MetabolomiQCsR.env$db$db <- "metabolomicsSQLDB"
MetabolomiQCsR.env$db$user <- "R_user"
MetabolomiQCsR.env$db$password <- "pass1234"
MetabolomiQCsR.env$db$host <- "127.0.0.1"

setwd("./QC4Metabolomics/Shiny App")
source("../init/init_db.R")

shiny::runApp(launch.browser = T)

Thanks a lot for the guidelines. Much appreciated.

from qc4metabolomics.

Hi @etrh. I Finally got around to putting it in a docker container. If you are still interested in testing let me know. Planning to add a proteowizard autoconverter too.

from qc4metabolomics.