search

nasqar / seuratv3wizard

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard
GNU General Public License v3.0
33 stars 14 forks source link

Can't browse cellbrowser, stuck at Prepared cellbrowser directory #10

Open clbenoit opened 4 years ago

clbenoit commented 4 years ago

Hello,

I successfully installed SeuratV3Wizard with its optional cellbrowser dependency, everything is working fine locally.

But then I tried to launch the app through a singularity image containing shiny-server and R 3.6.3 (From: rocker/shiny:3.6.3). The image contains also cellbrowser. And the app is launched as following :

singularity exec singularity_image.simg Rscript app. R

with app.R

appDir <- system.file('shiny', package = "SeuratV3Wizard"); shiny::shinyAppDir(appDir) Everything works fine until I try to "Generate cell browser data", it gets stuck at Prepared cellbrowser directory /tmp//pbmcellbrowser and never pass to the following step "Converting cellbrowser directory to html/json files" as I get when i run it locally.

Do you have any idea to get through this issue ?

Thanks you so much

Clément

aymanm commented 4 years ago

Hi, This is most likely due to updates in cellbrowser, as I have not tested it in sometime. I will look more into it and hopefully find a solution

aymanm commented 4 years ago

Have you tried installing this version? : sudo pip install cellbrowser=0.5.6

clbenoit commented 3 years ago

Specifying port here : 

          ExportToCellbrowser(pbmc, dir= folderpath, cb.dir=foldercbpath, reductions = "umap", markers.file = myValues$clusterFilePath, port = "5555")

And a bit of javascript here : 

         a("Launch Cellbrowser",href="#",onclick="javascript:window.open(port=5555)", class = "btn button button-3d button-pill button-action",target = "_blank"))

Did the job