[Bioc-devel] BiocParallel and Shiny

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Jul 7 14:26:31 CEST 2022

I think it should be straight-forward to use bpiterate() where the REDUCE function is evaluated locally. It might take a bit of care to make sure that the progress bar is actually informative – generally, increase the `tasks=` argument to the number of time you’d like the progress bar to be updated.

iter <- function(n) {
    ## return the numbers n, n-1, n-2, … until n < 0, and then return NULL
    function() {
        if (n < 0)
        else {
            n <<- n - 1
            n + 1

    function(i) { Sys.sleep(i/10); i },
    REDUCE = function(x, y) {
        c(x, y)
    BPPARAM = SnowParam(workers = 2, tasks = 10)

Replace `message()` to do whatever is required to iterate the progress bar in shiny. There is a `reduce.in.order=` argument that might be necessary to obtain results in order; I’m not exactly sure how this would impact a progress bar when, for instance, the early tasks take a long time…


From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Giulia Pais <giuliapais1 using gmail.com>
Date: Thursday, July 7, 2022 at 6:11 AM
To: Henrik Bengtsson <henrik.bengtsson using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] BiocParallel and Shiny
Thank you so much! I'll look into it, have a nice day

Giulia Pais
From: Henrik Bengtsson <henrik.bengtsson using gmail.com>
Sent: Thursday, July 7, 2022 11:59:36 AM
To: Giulia Pais <giuliapais1 using gmail.com>
Cc: Vincent Carey <stvjc using channing.harvard.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] BiocParallel and Shiny


If you use the DoparParam backend for BiocParallel with
doFuture::registerDoFuture(), then you have access to everything
available in the 'future' ecosystem.  This means you can use any of
the available future parallel backends, plus near-live progress
updates via the 'progressr' package. Progress signaled by 'progressr'
can be rendered in Shiny.

See https://progressr.futureverse.org/#biocparallelbplapply---parallel-lapply,
for an example how to use BiocParallel on top of the future framework
together with progress updates signaled by 'progressr'.

See https://progressr.futureverse.org/reference/withProgressShiny.html
for progressr::withProgressShiny(), which is a plug-in replacement for
shiny::withProgress().  Run example("withProgressShiny", package =
"progressr") for an example.

I gave a short presentation on progressr, with a focus on its use
together with future, at eRum 2020. The talk is available at
https://www.jottr.org/2020/07/04/progressr-erum2020-slides/.  It might
give some more insight on how it all works.

Hope this helps,


On Thu, Jul 7, 2022 at 11:51 AM Giulia Pais <giuliapais1 using gmail.com> wrote:
> Hi, thanks for the reply.
> Yes I�ve looked at this article, it seems to me like I have to access to the �status� of a worker in order to do that, correct?
> I mean, is there a way through BiocParallel interface in which I can receive a notification when a worker has finished a task? It is not clear to me how BiocParallel manages to update the progress bar internally � I guess the mechanism is similar to the one I described: distribute workload � when a worker has finished a task notify and update progress bar by one tick.
> I�m honestly not too practical with asynch task management in R, sorry.
> Thank you
> From: Vincent Carey <stvjc using channing.harvard.edu>
> Date: Thursday, July 7, 2022 at 11:40
> To: Giulia Pais <giuliapais1 using gmail.com>
> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] BiocParallel and Shiny
> Interesting question.  Have you looked at https://shiny.rstudio.com/articles/progress.html ...?  There is
> also a file called progress.R in BiocParallel/R folder.  Probably some new code needs to be written
> to connect information from the BiocParallel activities to the server so incProgress is run as needed.
> On Thu, Jul 7, 2022 at 4:48 AM Giulia Pais <giuliapais1 using gmail.com<mailto:giuliapais1 using gmail.com>> wrote:
> Hello,
> I have a question on the use of BiocParallel with Shiny: I would like to show a progress bar on the UI much like the standard progress bar that can be set in functions like bplapply() � is it possible to do it and how? I haven�t found anything on the topic in the documentation unfortunately.
> Thanks in advance,
> Giulia Pais
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