How to install systemPipe Workflows

Starting with pre-configured workflow templates

To test workflows quickly or design new ones from existing templates, users can generate with a single command workflow instances fully populated with sample data and parameter files required for running a chosen workflow.

Load one of the available workflows into your current working directory. The following does this for the varseq workflow template. The name of the resulting workflow directory can be specified under the mydirname argument. The default NULL uses the name of the chosen workflow. An error is issued if a directory of the same name and path exists already.

library("systemPipeRdata") 
genWorkenvir(workflow="systemPipeR/SPvarseq", mydirname=NULL)
setwd("varseq")

On Linux and OS X systems the same can be achieved from the command-line of a terminal with the following commands.

$ Rscript -e "systemPipeRdata::genWorkenvir(workflow='systemPipeR/SPvarseq', mydirname=NULL)"

Check availability of workflow templates

A collection of workflow templates are available, and it is possible to browse the current availability, as follows:

availableWF(github = TRUE)
## $systemPipeRdata
## [1] "chipseq" "new"     "riboseq" "rnaseq"  "varseq" 
## 
## $github
##                  workflow                       branches version
## 1   systemPipeR/SPchipseq                         master release
## 2   systemPipeR/SPriboseq                         master release
## 3    systemPipeR/SPrnaseq cluster, master, singleMachine release
## 4    systemPipeR/SPvarseq                         master release
## 5   systemPipeR/SPclipseq                         master   devel
## 6    systemPipeR/SPdenovo                         master   devel
## 7 systemPipeR/SPmetatrans                         master   devel
## 8 systemPipeR/SPmethylseq                         master   devel
## 9  systemPipeR/SPmirnaseq                         master   devel
##                                         html       description
## 1   https://github.com/systemPipeR/SPchipseq Workflow Template
## 2   https://github.com/systemPipeR/SPriboseq Workflow Template
## 3    https://github.com/systemPipeR/SPrnaseq Workflow Template
## 4    https://github.com/systemPipeR/SPvarseq Workflow Template
## 5   https://github.com/systemPipeR/SPclipseq Workflow Template
## 6    https://github.com/systemPipeR/SPdenovo Workflow Template
## 7 https://github.com/systemPipeR/SPmetatrans Workflow Template
## 8 https://github.com/systemPipeR/SPmethylseq Workflow Template
## 9  https://github.com/systemPipeR/SPmirnaseq Workflow Template

This function returns the list of workflow templates available within the package and systemPipeR Project Organization on GitHub. Each one listed template can be created as described above.

The workflow template choose from Github will be installed as an R package, and also it creates an environment with all the settings and files to run the demo analysis.

genWorkenvir(workflow="systemPipeR/SPrnaseq", mydirname="NULL")
setwd("systemPipeVARseq")

Besides, it is possible to choose different versions of the workflow template, defined through other branches on the GitHub Repository. By default, the master branch is selected, however, it is possible to define a different branch with the ref argument.

genWorkenvir(workflow="systemPipeR/SPrnaseq", ref = "singleMachine")
setwd("systemPipeRNAseq")