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")