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ruggleslab / jukebox

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how to #3

Closed lmanchon closed 5 years ago

lmanchon commented 5 years ago

--Hi,

i'm looking for manual or README file to install server on local system.

thany you --

jcooperdevlin commented 5 years ago

Hi!

WHAM! can be run locally in an R session with the server.R, ui.R and global.R scripts listed in the source code on GitHub.

We host our application through shinyApps and therefore do not have a dedicated server as of yet. Does this answer your question?

lmanchon commented 5 years ago

yes, but how to load the R files ? Do i need to put them in a dedicated folder ? thank you --

jcooperdevlin commented 5 years ago

Yes, I suggest pulling the wham_v1 repository to your local computer and then opening either the server.R or ui.R scripts in an rstudio session and selecting "Run App". This should work as long as all libraries and dependencies are installed.

lmanchon commented 5 years ago

ok, i'm going to do that. And another question about Humann2 output files: I have 3 output files from Humann2 analysis:

which of them is required by wham ?

jcooperdevlin commented 5 years ago

The gene families or pathway abundance will work with WHAM! But you will need to run the appropriate conversation scripts listed in the source code, to go from humann2 to a wham ready file format.

lmanchon commented 5 years ago

seems not working with R version 3.5.1: Warning message: package ‘rPython’ is not available (for R version 3.5.1)

source("D:\wham_v1\global.R") Error in library(rPython) : aucun package nommé ‘rPython’ n'est trouvé source("D:\wham_v1\ui.R") Error in loadingLogo("https://www.youtube.com/watch?v=pIgZ7gMze7A", "wham_logo_trans.png", : impossible de trouver la fonction "loadingLogo"

jcooperdevlin commented 5 years ago

I believe you can comment out the rPython library. This should not effect the application. However, I have not compiled our application as a standalone R package yet so there will be some dependencies that will need to be downloaded for specific R versions. WHAM! was built in R 3.4.1

lmanchon commented 5 years ago

okay good. thank you --

lmanchon commented 5 years ago

something strange on windows, i sourced the 3 files with no problems: source("D:\wham_v1\global.R") source("D:\wham_v1\ui.R") source("D:\wham_v1\server.R")

and nothing occurs

jcooperdevlin commented 5 years ago

I believe you would still need to run the actual application, "shiny::runApp()"

lmanchon commented 5 years ago

yes, it works now. thank you so much.