Add docker image for portability

[tyronechen]

Hi MBP, thanks for this useful tool

• Previously used the version from commit 173082f and found it very helpful
• Unfortunately ran into some libR.so issues during lattice compilation in some machines
  • if R version is not compiled with --enable-R-shlib
• Made this Docker image and github workflow to work around that
  • but note that the versions wont align 100% with renv
• Also added qs2

On an unrelated note, i saw that some paths were hardcoded in the latest commit post processing which results in the shiny app breaking
(I can open a separate pull request for this later on)

server.R:sc1conf = readRDS("sc1conf.rds")
ui.R:sc1conf = readRDS("sc1conf.rds")

[tyronechen]

On an unrelated note, i saw that some paths were hardcoded in the latest commit post processing which results in the shiny app breaking (I can open a separate pull request for this later on)

server.R:sc1conf = readRDS("sc1conf.rds")
ui.R:sc1conf = readRDS("sc1conf.rds")

Sorry my mistake, ignore this part. I was using the wrong assay (specified SCT instead of log-normalised RNA).

[LPerlaza]

Hi Tyron,

Thanks for trying the tool. We are working on adding a container for this.

You should be running theapp.R and not the server.R or ui.R. ShinyCellModular is meant to work in modules but it is a reformatting of the original ShinyCell. The app.R is the actual app that calls the modules. After using prepShinyCellModular() and useShinyCellModular() your server.R andui.R should turn into server.R.bak and ui.R.bak. I have not added yet any alternatives for SCT assays; but it will be included in the near future

[tyronechen]

Hi Tyron,

Thanks for trying the tool. We are working on adding a container for this.

Thanks for making this tool!

You should be running theapp.R and not the server.R or ui.R. ShinyCellModular is meant to work in modules but it is a reformatting of the original ShinyCell. The app.R is the actual app that calls the modules. After using prepShinyCellModular() and useShinyCellModular() your server.R andui.R should turn into server.R.bak and ui.R.bak. I have not added yet any alternatives for SCT assays; but it will be included in the near future

No worries, thanks for the clarification. I successfully ran the steps and hosted the shiny app for log normalised RNA assay data using the SCT umap coordinates.

[LPerlaza]

AWESOME! Thanks for sharing!