GitHub - flow-r/flowr: Robust and efficient workflows using a simple language agnostic approach (original) (raw)

Latest documentation: flow-r.github.io/flowr

Flowr framework allows you to design and implement complex pipelines, and deploy them on your institution's computing cluster. This has been built keeping in mind the needs of bioinformatics workflows. However, it is easily extendable to any field where a series of steps (shell commands) are to be executed in a (work)flow.

Highlights

• No new syntax or language. Put all shell commands as a tsv file called flow mat.
• Define the flow of steps using a simple tsv file (serial, scatter, gather, burst...) called flow def.
• Works on your laptop/server or cluster (/cloud).
• Supports multiple cluster computing platforms (torque, lsf, sge, slurm ...), cloud (star cluster) OR a local machine.
• One line installation (install.packages("flowr"))
• Reproducible and transparent, with cleanly structured execution logs
• Track and re-run flows
• Lean and Portable, with easy installation
• Fine grain control over resources (CPU, memory, walltime, etc.) of each step.

Example

A few lines, to get started

Official stable release from CRAN (updated every other month)

visit flow-r.github.io/flowr/install for more details

install.packages("flowr", repos = "http://cran.rstudio.com")

or a latest version from DRAT, provide cran for dependencies

install.packages("flowr", repos = c(CRAN="http://cran.rstudio.com", DRAT="http://sahilseth.github.io/drat"))

library(flowr) ## load the library setup() ## copy flowr bash script; and create a folder flowr under home.

Run an example pipeline

style 1: sleep_pipe() function creates system cmds

flowr run x=sleep_pipe platform=local execute=TRUE

style 2: we start with a tsv of system cmds

get example files

wget --no-check-certificate http://raw.githubusercontent.com/sahilseth/flowr/master/inst/pipelines/sleep_pipe.tsv wget --no-check-certificate http://raw.githubusercontent.com/sahilseth/flowr/master/inst/pipelines/sleep_pipe.def

submit to local machine

flowr to_flow x=sleep_pipe.tsv def=sleep_pipe.def platform=local execute=TRUE

submit to local LSF cluster

flowr to_flow x=sleep_pipe.tsv def=sleep_pipe.def platform=lsf execute=TRUE

Example pipelines inst/pipelines

Resources

• For a quick overview, you may browse through, these introductory slides.
• The overview provides additional details regarding the ideas and concepts used in flowr
• We have a tutorial which can walk you through creating a new pipeline
• Additionally, a subset of important functions are described in the package referencepage
• You may follow detailed instructions on installing and configuring
• You can use flow creator: https://sseth.shinyapps.io/flow_creator), a shiny app to aid in designing a shiny new flow. This provides a good example of the concepts

Updates

This package is under active-development, you may watch for changes using the watch link above.

Feedback

Please feel free to raise a github issue with questions and comments.

Acknowledgements

• Jianhua Zhang
• Samir Amin
• Roger Moye
• Kadir Akdemir
• Ethan Mao
• Henry Song
• An excellent resource for writing your own R packages:r-pkgs.org