It seems that with packrat, the user can snapshot their environment, but I don't see a way to create a snapshot with an ID mapped to a particular Rmd document That way I can still work on other project (dev or analysis) on my working environment in RStudio server. (May be launched form a code chunk I think).įor this kind of use case, I usually "deploy" my Rmd document (or R script) in an execution environment different from my development RStudio Server where I launch the execution ( rmarkdown::render for exemple). Otherwise, you may use to compute some code in a background process for example. RStudio Server Pro has this feature too open multiple session. if you want to work on another project while a R process compute code from a Rmarkdown, why don't you use another new R session ? If I try to do with with Rmarkdown + knitr, can I call a bash job in a bash code chunk and then switch to a different project while that bash job takes hours or days to run, or am I stuck either waiting for the bash job to complete, or keeping the bash job external from Rmarkdown + knitr because it takes too long In other words, does Rmarkdown + knitr really work for documenting a bioinformatics pipeline? I know that I could use snakemake or other pipelining software for such cases (and I sometimes do this), but that can require a lot of setup, which isn't needed for relatively simple pipelines. If I try to do with with Rmarkdown + knitr, can I call a bash job in a bash code chunk and then switch to a different project while that bash job takes hours or days to run, or am I stuck either waiting for the bash job to complete, or keeping the bash job external from Rmarkdown + knitr because it takes too long? With Jupyter Notebooks, I can document all bash calls to software for genome assembly, BLAST, metagenome analyses, etc., and these bash jobs can take a long time to run (eg., a long BLAST job). could definitely help with making long-running jobs run quicker, but I am worried about dealing with external bioinformatics software that can take a while run. Thanks for the suggestions! futures, doParallel, batchtools, etc.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |