[Bioc-devel] Using BioC vignettes as Jupyter Notebooks

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Jul 2 11:50:08 CEST 2019

Do you think this approach could be re-cast in the same way that https://github.com/Bioconductor/bioconductor_full has done, so that the container has all the software to _support_ the packages needed for the jupyter notebook, but that the user must do some kind of initialization to install the R libraries? In this way there would be one container instead of 1750, and it would not be heavy?

One idea that we've been exploring is making _binary_ versions of Bioc packages available that are compatible with bioconductor_full, so that package installation would sometimes be much faster (a simple download, rather than compilation).


On 7/2/19, 10:52 AM, "Bioc-devel on behalf of Neumann, Steffen" <bioc-devel-bounces using r-project.org on behalf of sneumann using ipb-halle.de> wrote:

    last week over a beer some of us realized that (technically)
    it is possible to run most[1] Rmd vignettes as Jupiter Notebook. 
    So I created https://github.com/sneumann/bioc_notebooks 
    which takes some example packages and creates a Docker container 
    with converted vignettes. The resulting container 
    can be hosted locally, or on the binder system (see README).
    We found this to be fun, and it could be used 
    as a great training resource. Only downside is 
    that the resulting containers are not exactly light-weight.
    [1] See the issue in the repo where it fails. 
    IPB Halle                    AG Massenspektrometrie & Bioinformatik
    Dr. Steffen Neumann          http://www.IPB-Halle.DE
    Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
    06120 Halle                       +49 (0) 345 5582 - 0
    sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
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