How to install systemPipe Workflows

Starting with pre-configured stable 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="varseq")
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='varseq')"

After the command above, the directory varseq will be created in the current working directory. The structure of the directory is as follows:

varseq/
├── batchtools.slurm.tmpl
├── bibtex.bib
├── data
├── param
├── results
├── systemPipeVARseq.html
├── systemPipeVARseq.R
├── systemPipeVARseq.Rmd
├── targetsPE.txt
├── targetsPE_varseq.txt
└── targets.txt

Check availability of workflow templates

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

availableWF()

## Available Workflow Templates in systemPipeRdata:
## Name         Description
## ------------------------------------
## chipseq      ChIP-seq
## new          New Empty Workflow
## riboseq      Ribosome Profiling
## rnaseq       RNA-seq
## SPblast      BLAST
## SPcheminfo   Chemical Informatics
## SPscrna      Single-cell RNA-seq
## varseq       Variant Calling

In addition, one can check experimental workflows available in the Github Organization systemPipeR as follows:

availableWF(github = TRUE)

## Checking templates in systemPipeR GitHub, please wait ...
## Available Workflow Templates in systemPipeRdata:
## Name         Description
## ------------------------------------
## chipseq      ChIP-seq
## new          New Empty Workflow
## riboseq      Ribosome Profiling
## rnaseq       RNA-seq
## SPblast      BLAST
## SPcheminfo   Chemical Informatics
## SPscrna      Single-cell RNA-seq
## varseq       Variant Calling
## Experimental Workflow Templates in systemPipeR GitHub Organization:
##        Workflow                                     Download URL
## 1     SPatacseq     https://github.com/systemPipeR/SPatacseq.git
## 2     SPclipseq     https://github.com/systemPipeR/SPclipseq.git
## 3      SPdenovo      https://github.com/systemPipeR/SPdenovo.git
## 4         SPhic         https://github.com/systemPipeR/SPhic.git
## 5   SPmetatrans   https://github.com/systemPipeR/SPmetatrans.git
## 6   SPmethylseq   https://github.com/systemPipeR/SPmethylseq.git
## 7    SPmirnaseq    https://github.com/systemPipeR/SPmirnaseq.git
## 8 SPpolyriboseq https://github.com/systemPipeR/SPpolyriboseq.git

Installation of experimental workflows can done by git clone the repository.

git clone <URL FROM THE TABLE ABOVE>
cd <REPO_NAME>

After the installation, start the SPR project as others.

library(systemPipeR)
sal <- SPRproject()
sal <- importWF(sal, file_path = "workflow_name.Rmd")