This 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 to process big data.
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## Latest stable release from CRAN (updated every other month) ## visit docs.flowr.space/install for more details ## for a latest official version (from CRAN) Rscript -e 'install.packages("flowr", repos = c(CRAN="http://cran.rstudio.com"))' ## Latest stable release from DRAT (updated every other week); CRAN for dependencies Rscript -e 'install.packages("flowr", repos = c(CRAN="http://cran.rstudio.com", DRAT="http://sahilseth.github.io/drat"))' Rscript -e 'library(flowr);setup()' # 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