Notebooks: using (my own) tools in docker

shbriefshbrief New YorkMember

Hi! I'm trying to move my analysis workflow to R notebook in FireCloud.
Is there any way to incorporate my own tools in docker into FC's notebook? Thanks!

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  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @shbrief I will look into the details and get back to you with an answer soon!

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @shbrief

    I wanted to ask a follow up question. Does your R notebook call your docker or is your R notebook inside of your docker?

    Thanks for any info.

  • shbriefshbrief New YorkMember

    Hi @AdelaideR, I'm wondering whether R notebook can call my docker.

  • akmanningakmanning United StatesMember

    Here’s an example where I run an R notebook, and rendered to html within a WDL task. Is this what you are looking to do?

        workflow regionalsummary {
        call taskregionalsummary
       }
    
       task taskregionalsummary {
            String study
            File regionalscript
            File results
        String label
        File inputfilescript
        File functionsfile
        File gtexadiposesubfile
        File gtexadiposevisfile
        File gtexpancreasfile
        File gtexmusclefile
        File gtexliverfile
        String pvalthreshold
        String mafthreshold
    
            command {
            ls -la && Rscript -e 'rmarkdown::render("${regionalscript}",output_file="${label}_regional.html",output_dir="/cromwell_root/")' ${results} ${study} ${label} ${inputfilescript} ${functionsfile} ${gtexadiposesubfile} ${gtexadiposevisfile} ${gtexpancreasfile} ${gtexmusclefile} ${gtexliverfile} ${pvalthreshold} ${mafthreshold} && ls -la && ls -la /cromwell_root/ 
            }
    
            output {
                    File regional_html = "${label}_regional.nb.html"
            }
            runtime {
                docker: "bioconductor/release_core2"
                memory: "40GB"
                disks: "local-disk 100 SSD"
    
        }
    
    
  • shbriefshbrief New YorkMember

    @akmanning Thanks! This will be a useful reference for my work. :wink:

    @SChaluvadi Thanks, this answers my question! It'll be nice if I can call Docker in my R script. Looking forward to it. :smile:

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