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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.
## 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
This package is under active-development, you may watch for changes using the watch link above.
Please feel free to raise a github issue with questions and comments.
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