systemPipeRdata

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# systemPipeRdata
### Daniela Cassol
### <h3>
University of California Riverside
<h3/>
### <h3>
2020/08/28 (updated: 2021-02-08)
<h3/>

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## Outline

#### Introduction
#### Live Demo
    - Install Package
    - Quick Start
    - Directory Structure
    - Workflow Collection
    - Install Workflow Template

---
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# Introduction

---
## Introduction

[_systemPipeRdata_](http://www.bioconductor.org/packages/release/data/experiment/html/systemPipeRdata.html) is a helper package to generate with a single command workflow templates 
that are intended to be used by its parent package [_systemPipeR_](http://www.bioconductor.org/packages/release/bioc/html/systemPipeR.html).
 
Includes sample data for testing.

Users can create *new workflows* or change and extend existing ones.

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# Live Demo

---
## Install Package

Install the **systemPipeRdata** package from [Bioconductor](http://www.bioconductor.org/packages/release/data/experiment/html/systemPipeRdata.html):

```r
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("systemPipeRdata")
```

### Load Package and Documentation

Load package:

```r
library("systemPipeRdata")
```

Access help:

```r
library(help="systemPipeRdata")
vignette("systemPipeRdata")
```

---
## Quick Start

Generate workflow template:

```r
genWorkenvir(workflow="varseq")
setwd("varseq")
```

Command-line alternative for generating workflow environments:

```bash
$ Rscript -e "systemPipeRdata::genWorkenvir(workflow='varseq', mydirname=NULL, url=NULL, urlname=NULL)"
```

---
## Directory Structure

The workflow templates generated by _`genWorkenvir`_ contain the following preconfigured directory structure:

---
## Workflows Collection

Browse pipelines that are currently available as part of the *systemPipeR* toolkit

.small[
| WorkFlow | Description | Version | GitHub | CI Testing | 
|:-----------------------:|:----------------:|:----------------:|:--------------------:|:-------------------------------:|
| [systemPipeChIPseq](https://systempiper.github.io/systemPipeChIPseq/articles/systemPipeChIPseq.html) | ChIP-Seq Workflow Template | v1.0 <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/check.png" align="center" style="width:20px;" /> | <a href="https://github.com/systemPipeR/systemPipeChIPseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeChIPseq/workflows/R-CMD-check/badge.svg) |
| [systemPipeRIBOseq](https://systempiper.github.io/systemPipeRIBOseq/articles/systemPipeRIBOseq.html) | RIBO-Seq Workflow Template | v1.0 <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/check.png" align="center" style="width:20px;" /> | <a href="https://github.com/systemPipeR/systemPipeRIBOseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeRIBOseq/workflows/R-CMD-check/badge.svg) |
| [systemPipeRNAseq](https://systempiper.github.io/systemPipeRNAseq/articles/systemPipeRNAseq.html) | RNA-Seq Workflow Template | v1.0 <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/check.png" align="center" style="width:20px;" /> | <a href="https://github.com/systemPipeR/systemPipeRNAseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeRNAseq/workflows/R-CMD-check/badge.svg) |
| [systemPipeVARseq](https://systempiper.github.io/systemPipeVARseq/articles/systemPipeVARseq.html) | VAR-Seq Workflow Template | v1.0 <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/check.png" align="center" style="width:20px;" /> | <a href="https://github.com/systemPipeR/systemPipeVARseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeVARseq/workflows/R-CMD-check/badge.svg) |
| [systemPipeMethylseq](https://github.com/systemPipeR/systemPipeMethylseq) | Methyl-Seq Workflow Template | devel <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/devel.png" align="center" style="width:25px;" /> | <a href="https://github.com/systemPipeR/systemPipeMethylseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeMethylseq/workflows/R-CMD-check/badge.svg) |
| [systemPipeDeNovo](https://github.com/systemPipeR/systemPipeDeNovo) | De novo transcriptome assembly Workflow Template | devel <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/devel.png" align="center" style="width:25px;" /> | <a href="https://github.com/systemPipeR/systemPipeDeNovo"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeDeNovo/workflows/R-CMD-check/badge.svg) |
| [systemPipeCLIPseq](https://github.com/systemPipeR/systemPipeCLIPseq) | CLIP-Seq Workflow Template | devel <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/devel.png" align="center" style="width:25px;" /> | <a href="https://github.com/systemPipeR/systemPipeCLIPseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeCLIPseq/workflows/R-CMD-check/badge.svg) |
| [systemPipeMetaTrans](https://github.com/systemPipeR/systemPipeMetaTrans) | Metatranscriptomic Sequencing Workflow Template | devel <img src="https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/devel.png" align="center" style="width:25px;" /> | <a href="https://github.com/systemPipeR/systemPipeMetaTrans"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | ![R-CMD-check](https://github.com/systemPipeR/systemPipeMetaTrans/workflows/R-CMD-check/badge.svg) |
]

---
## Install Workflow

Check the workflow template availability

```r
availableWF(github = TRUE)

# $systemPipeRdata
# [1] "chipseq" "new"     "riboseq" "rnaseq"  "varseq" 
# 
# $github
#                          workflow                       branches version                                               html       description
# 1   systemPipeR/systemPipeChIPseq                         master release   https://github.com/systemPipeR/systemPipeChIPseq Workflow Template
# 2   systemPipeR/systemPipeRIBOseq                         master release   https://github.com/systemPipeR/systemPipeRIBOseq Workflow Template
# 3    systemPipeR/systemPipeRNAseq cluster, master, singleMachine release    https://github.com/systemPipeR/systemPipeRNAseq Workflow Template
# 4    systemPipeR/systemPipeVARseq                         master release    https://github.com/systemPipeR/systemPipeVARseq Workflow Template
# 5   systemPipeR/systemPipeCLIPseq                         master   devel   https://github.com/systemPipeR/systemPipeCLIPseq Workflow Template
# 6    systemPipeR/systemPipeDeNovo                         master   devel    https://github.com/systemPipeR/systemPipeDeNovo Workflow Template
# 7 systemPipeR/systemPipeMetaTrans                         master   devel https://github.com/systemPipeR/systemPipeMetaTrans Workflow Template
# 8 systemPipeR/systemPipeMethylseq                         master   devel https://github.com/systemPipeR/systemPipeMethylseq Workflow Template
```

---
## Install Workflow

Install Workflow Template from [*systemPipeR* Organization](https://github.com/systemPipeR):

```r
genWorkenvir(workflow="systemPipeR/systemPipeVARseq", mydirname=NULL)

# [1] "Package systemPipeVARseq is successfully installed!"
# [1] "The 'demo data'was successfully copied to your project."
# [1] "The 'param' directory was successfully copied to your project."
# [1] "Generated systemPipeVARseq directory. Next run in systemPipeR/systemPipeVARseq directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette."
```

Install Workflow Template with a specific *R Markdown* file:

```r
genWorkenvir(workflow="systemPipeR/systemPipeRNAseq", mydirname="rnaseq",
             url = "https://raw.githubusercontent.com/systemPipeR/systemPipeRNAseq/cluster/vignettes/systemPipeRNAseq.Rmd",
             urlname = "rnaseq_V-cluster.Rmd")
```

---
## Dynamic Workflow Template

Create dynamic Workflow Templates with *RStudio*

`File -> New File -> R Markdown -> From Template`
.center[
<img src="rstudio.png" height="425px" class="center" />
]

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# Thanks!

Browse source code at <a href="https://github.com/tgirke/systemPipeRdata/"> </a>

Ask a question about systemPipeRdata at Bioconductor Support Page
<a href="https://support.bioconductor.org/t/systempiper/"></a>

*systemPipeRdata* at [Bioconductor](http://www.bioconductor.org/packages/release/data/experiment/html/systemPipeRdata.html)

[https://systempipe.org/](https://systempipe.org/)