Daniela Cassol" -institute: "
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-date: "2020/10/20 (updated: 2021-04-25)"
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----
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diff --git a/content/en/presentations/SPR/SPR_project.md b/content/en/presentations/SPR/SPR_project.md
new file mode 100644
index 000000000..b223f74e5
--- /dev/null
+++ b/content/en/presentations/SPR/SPR_project.md
@@ -0,0 +1,793 @@
+---
+title: _systemPipeR_
+subtitle: ""
+author: "
Daniela Cassol"
+institute: "University of California Riverside"
+date: "2020/10/20 (updated: 2021-04-25)"
+output:
+ xaringan::moon_reader:
+ css: ["css/xaringan-themer.css", "css/custom.css"]
+ lib_dir: libs
+ nature:
+ highlightStyle: github
+ highlightLines: true
+ countIncrementalSlides: true
+ # seal: false
+---
+
+layout: true
+background-image: url(https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/systemPipeR.png)
+background-position: 99% 1%
+background-size: 10%
+
+
+
+
+
+
+
+---
+class: middle
+
+## Outline
+
+#### Introduction
+#### Design
+#### How to run a Workflow
+#### Workflows Tutorial
+#### Live Demo
+
+
+
+
+---
+class: inverse, center, middle
+
+# Introduction
+
+
+---
+## Introduction
+
+
+[_systemPipeR_](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html) provides a suite of R/Bioconductor packages for designing, building and running end-to-end analysis workflows on local machines, HPC clusters and cloud systems, while generating at the same time publication quality analysis reports
+
+
+_systemPipeR_ offers many utilities to build, control, and execute
+workflows entirely from R
+
+
+The environment takes advantage of central community S4 classes of the Bioconductor ecosystem
+
+
+Workflows are managed by generic workflow management containers supporting both analysis routines implemented in R code and/or command-line software
+
+
+Simple annotation system targets
+
+
+---
+### systemPipeR’s Core Functionalities
+
+.center[
+
+]
+
+
+
+---
+## Structural Features
+
+--
+.left-column[
+#### WF infrastructure
+]
+
+.right-column[
+*systemPipeR* offers many utilities to build, control, and execute
+workflows entirely from R. The environment takes advantage of central community S4 classes
+of the Bioconductor ecosystem. Workflows are managed by generic workflow management
+containers supporting both analysis routines implemented in R code and/or command-line
+software. A layered monitoring infrastructure is provided to design, control and debug each
+step in a workflow. The run environment allows to execute workflows entirely or with a
+intuitive to use step-wise execution syntax using R’s standard subsetting syntax
+(runWF(sys[1:3])) or pipes (%>%).
+]
+
+---
+
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+]
+
+.right-column[
+An important feature of systemPipeR is support for
+running command-line software by adopting the Common Workflow Language (CWL). The
+latter is a widely adopted community standard for describing analysis workflows. This design
+offers several advantages such as:
+
+
+seamless integration of most command-line software
+
+
+support to run systemPipeR workflows from R or many other popular computer languages
+
+
+efficient sharing of workflows across different workflow environments.
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+]
+
+.right-column[
+The processing time of workflows can be greatly reduced by making use
+of parallel evaluations across several CPU cores on single machines, or multiple nodes of
+computer clusters and cloud-based systems. systemPipeR simplifies these parallelization tasks
+without creating any limitations for users who do not have access to high-performance
+computer resources
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+]
+
+.right-column[
+*systemPipeR’s* reporting infrastructure
+includes three types of interconnected reports each serving a different purpose:
+
+
+a scientific report, based on R Markdown, contains all scientifically relevant results
+
+
+a technical report captures all technical information important for each workflow step, including parameter
+settings, software versions, and warning/error messages, etc.
+
+
+a visual report depicts the entire workflow topology including its run status in form of a workflow graph
+
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+#### Shiny Web Interface
+]
+
+.right-column[
+Recently, the systemPipeShiny package has been added that allows
+users to design workflows in an interactive graphical user interface (GUI). In addition to
+designing workflows, this new interface allows users to run and to monitor workflows in an
+intuitive manner without the need of knowing R.
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+#### Shiny Web Interface
+#### Workflow Templates
+]
+
+.right-column[
+A rich set of end-to-end workflow templates is provided by this
+project for a wide range omics applications. In addition, users can contribute and share their
+workflows with the community by submitting them to a central GitHub repository
+]
+
+
+---
+## Important Functions
+
+.small[
+| Function Name | Description | Category |
+|-------------------|-----------------------------------------------------------------------------------------------------------------------|-----------------|
+| `genWorkenvir` | Generates workflow templates provided by systemPipeRdata helper package / or from the individuals’ pipelines packages | Accessory |
+| `loadWorkflow` | Constructs `SYSargs2` object from CWL param and targets files | ``SYSargs2`` |
+| `renderWF` | Populate all the command-line in an `SYSargs2` object | ``SYSargs2`` |
+| `subsetWF` | Subsetting `SYSargs2` class slots | ``SYSargs2`` |
+| `runCommandline` | Executes command-line software on samples and parameters specified in `SYSargs2` object | ``SYSargs2`` |
+| `clusterRun` | Runs command-line software in parallel mode on a computer cluster | ``SYSargs2`` |
+| `writeTargetsout` | Write updated targets out to file/Generate targets file with reference | ``SYSargs2`` |
+| `output_update` | Updates the output files paths in the `SYSargs2` object | ``SYSargs2`` |
+| `singleYML` | Create automatically the `param.yml` | ``SYSargs2`` |
+| `createWF` | Create automatically `param.cwl` and the `param.yml` based on the command line | ``SYSargs2`` |
+| `config.param` | Custom configuration of the CWL param files from R | ``SYSargs2`` |
+]
+
+---
+## Important Functions
+
+.small[
+| Function Name | Description | Category |
+|-------------------|-----------------------------------------------------------------------------------------------------------------------|-----------------|
+| `initWF` | Constructs `SYSargsList` workflow control module (S4 object) from script file | ``SYSargsList`` |
+| `configWF` | Control of which step of the workflow will be run and the generation of the new RMarkdown | ``SYSargsList`` |
+| `runWF` | Runs all the R chunk define in the RMarkdown file or a subset, e.g. `runWF[1:3]` | ``SYSargsList`` |
+| `renderReport` | Render Scientific Report based on RMarkdown | ``SYSargsList`` |
+| `subsetRmd` | Write updated subset Rmarkdown of R chunk with text associate in the step selected | ``SYSargsList`` |
+| `plotWF` | Plot visual workflow designs and topologies with different graphical layouts | ``SYSargsList`` |
+| `statusWF` | Return the overview of the workflow steps computational status | ``SYSargsList`` |
+| `evalCode` | Turn eval option `TRUE` or `FALSE` on RMarkdown file | Accessory |
+| `tryCL` | Checks if third-party software or utility is installed and set in the PATH | Accessory |
+]
+
+
+
+
+
+
+---
+class: inverse, center, middle
+
+# Design
+
+---
+### Workflow Management Solutions
+
+
+*systemPipeR* central concept for designing workflows is **workflow
+management containers** (S4 class)
+
+
+*SYSargs2* controls workflow steps with input/output file operations
+
+
+*SYSargs2* requires a targets and a set of workflow definition files (here param.cwl and param.yml)
+
+
+
+
+
+*SYSargsList* objects organize one or many *SYSargs2*
+containers in a single compound object capturing all information required to run, control and
+monitor complex workflows from start to finish
+
+.center[
+
+]
+
+---
+## 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 
| 
|  |
+| [systemPipeRIBOseq](https://systempiper.github.io/systemPipeRIBOseq/articles/systemPipeRIBOseq.html) | RIBO-Seq Workflow Template | v1.0 | |  |
+| [systemPipeRNAseq](https://systempiper.github.io/systemPipeRNAseq/articles/systemPipeRNAseq.html) | RNA-Seq Workflow Template | v1.0 | |  |
+| [systemPipeVARseq](https://systempiper.github.io/systemPipeVARseq/articles/systemPipeVARseq.html) | VAR-Seq Workflow Template | v1.0 | |  |
+| [systemPipeMethylseq](https://github.com/systemPipeR/systemPipeMethylseq) | Methyl-Seq Workflow Template | devel 
| |  |
+| [systemPipeDeNovo](https://github.com/systemPipeR/systemPipeDeNovo) | De novo transcriptome assembly Workflow Template | devel | |  |
+| [systemPipeCLIPseq](https://github.com/systemPipeR/systemPipeCLIPseq) | CLIP-Seq Workflow Template | devel | |  |
+| [systemPipeMetaTrans](https://github.com/systemPipeR/systemPipeMetaTrans) | Metatranscriptomic Sequencing Workflow Template | devel | |  |
+]
+
+---
+class: inverse, center, middle
+
+# CWL
+
+---
+## CWL
+
+ **TODO:**
+Add section with CWL details
+
+.center[
+
+]
+
+---
+## CWL and SPR
+
+ **TODO:**
+How to use CWL definition with *systemPipeR*
+
+- *SYSargs2* instances are constructed from a *`targets`* file and two *`param`* file
+ - *`hisat2-mapping-se.cwl`* file contains the settings for running command-line software
+ - *`hisat2-mapping-se.yml`* file define all the variables to be input in the specific command-line step
+
+
+```r
+targets <- system.file("extdata", "targets.txt", package="systemPipeR")
+dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
+align <- loadWF(targets=targets, wf_file="hisat2-mapping-se.cwl",
+ input_file="hisat2-mapping-se.yml", dir_path=dir_path)
+align <- renderWF(align, inputvars=c(FileName="_FASTQ_PATH_", SampleName="_SampleName_"))
+
+## Instance of 'SYSargs2':
+## Slot names/accessors:
+## targets: 18 (M1A...V12B), targetsheader: 4 (lines)
+## modules: 2
+## wf: 0, clt: 1, yamlinput: 7 (components)
+## input: 18, output: 18
+## cmdlist: 18
+## WF Steps:
+## 1. hisat2-mapping-se.cwl (rendered: TRUE)
+```
+
+---
+## CWL and SPR
+
+## *`SYSargs2`* instance
+
+- Slots and accessor functions have the same names
+
+```r
+names(align)
+# [1] "targets" "targetsheader" "modules" "wf" "clt"
+# [6] "yamlinput" "cmdlist" "input" "output" "cwlfiles"
+# [11] "inputvars"
+```
+
+- *`cmdlist`* return command-line arguments for the specific software, here *`HISAT2`* for the first sample
+
+```r
+cmdlist(align)[1]
+# $M1A
+# $M1A$`hisat2-mapping-se.cwl`
+# [1] "hisat2 -S results/M1A.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446027_1.fastq.gz --threads 4"
+```
+
+- The output components of *`SYSargs2`* define all the expected output files for each step in the workflow; some of which are the input for the next workflow step
+
+
+```r
+output(align)[1]
+# $M1A
+# $M1A$`hisat2-mapping-se.cwl`
+# [1] "results/M1A.sam"
+```
+
+---
+class: inverse, center, middle
+
+# Metadata
+
+---
+### *Targets* file organizes samples
+
+- Structure of *`targets`* file for single-end (SE) library
+
+```r
+targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:3,1:4]
+```
+
+```
+## FileName SampleName Factor SampleLong
+## 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A
+## 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B
+## 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A
+```
+
+- Structure of *`targets`* file for paired-end (PE) library
+
+```r
+targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:3,1:5]
+```
+
+```
+## FileName1 FileName2 SampleName Factor
+## 1 ./data/SRR446027_1.fastq.gz ./data/SRR446027_2.fastq.gz M1A M1
+## 2 ./data/SRR446028_1.fastq.gz ./data/SRR446028_2.fastq.gz M1B M1
+## 3 ./data/SRR446029_1.fastq.gz ./data/SRR446029_2.fastq.gz A1A A1
+## SampleLong
+## 1 Mock.1h.A
+## 2 Mock.1h.B
+## 3 Avr.1h.A
+```
+
+---
+### Integration with *SummarizedExperiment*
+
+- Integrates *targets* files and count table from *systemPipeR* to a *SummarizedExperiment* object
+
+
+```r
+## Create an object with targets file and comparison and count table
+sprSE <- SPRdata(targetspath = targetspath, cmp=TRUE)
+metadata(sprSE)
+# $version
+# [1] ‘1.23.9’
+#
+# $comparison
+# $comparison$CMPset1
+# [,1] [,2]
+# [1,] "M1" "A1"
+# [2,] "M1" "V1"
+# [3,] "A1" "V1"
+# [4,] "M6" "A6"
+
+colData(sprSE)
+# DataFrame with 18 rows and 6 columns
+# FileName SampleName Factor SampleLong
+#
+# M1A ./data/SRR446027_1.f.. M1A M1 Mock.1h.A
+# M1B ./data/SRR446028_1.f.. M1B M1 Mock.1h.B
+# ... ... ... ... ...
+# M12B ./data/SRR446040_1.f.. M12B M12 Mock.12h.B
+```
+
+---
+class: inverse, center, middle
+
+# 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("systemPipeR")
+```
+
+### Load Package and Documentation
+
+
+Load package:
+
+
+```r
+library("systemPipeR")
+```
+
+
+Access help:
+
+
+```r
+library(help="systemPipeR")
+vignette("systemPipeR")
+```
+
+---
+## Quick Start
+
+### Load Sample Workflow
+
+
+*systemPipeRdata*
+
+- Helper package to generate with a single command workflow templates for *systemPipeR*
+- Includes sample data for testing
+- User can create new workflows or change and extend existing ones
+- Template Workflows:
+ - Sample workflows can be loaded with the *`genWorkenvir`* function from **systemPipeRdata**
+
+
+Generate workflow template:
+
+
+```r
+library(systemPipeRdata)
+genWorkenvir(workflow="rnaseq")
+setwd("rnaseq")
+```
+
+
+More details about *systemPipeRdata* package [here](https://systempipe.org/pages/SPRdata_intro/SPRdata_intro#1)
+
+---
+## 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
+```
+
+---
+## Dynamic Workflow Template
+
+
+Create dynamic Workflow Templates with *RStudio*
+
+
+`File -> New File -> R Markdown -> From Template`
+.center[
+
+]
+
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+]
+
+.right-column[
+
+```r
+library(systemPipeR)
+targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:4,1:4]
+```
+
+```
+## FileName SampleName Factor SampleLong
+## 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A
+## 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B
+## 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A
+## 4 ./data/SRR446030_1.fastq.gz A1B A1 Avr.1h.B
+```
+
+```r
+script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- initWF(script = script, targets = targetspath, overwrite = TRUE)
+# Project started with success: ./SYSproject and SYSconfig.yml were created.
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- configWF(sysargslist, input_steps = "1:3")
+sysargslist
+# Instance of 'SYSargsList':
+# WF Steps:
+# 1. Rmarkdown/HTML setting
+# 2. Introduction
+# 3. Samples and environment settings
+# 3.1. Environment settings and input data
+# 3.2. Required packages and resources
+# 3.3. Experiment definition provided by `targets` file
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+### `runWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- runWF(sysargslist, steps = "1:2")
+# Step: 1: Introduction --> DONE
+# Step: 2: Samples and environment settings --> DONE
+# Step: 2.1: Environment settings and input data --> DONE
+# Step: 2.2: Required packages and resources --> DONE
+# Step: 2.3: Experiment definition provided by `targets` file --> DONE
+```
+
+
+```r
+sysargslist <- runWF(sysargslist, steps = "ALL")
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+### `runWF`
+### `renderReport`
+]
+
+.right-column[
+
+```r
+sysargslist <- renderReport(sysargslist = sysargslist)
+```
+]
+
+---
+## How to Use Pipes `%>%`
+
+Consider the following example, in which the steps are the initialization, configuration and running the entire workflow.
+
+
+```r
+library(systemPipeR)
+sysargslist <- initWF(script ="systemPipeRNAseq.Rmd", overwrite = TRUE) %>%
+ configWF(input_steps = "1:6") %>%
+ runWF(steps = "1:2")
+```
+
+---
+class: inverse, center, middle
+
+# Project Updates
+
+---
+### *targets* x *SummarizedExperiment*
+
+Extension "SummarizedExperiment" methods:
+
+
+```r
+sprSE <- addAssay(sprSE, assay(countMatrix), xName="countMatrix")
+sprSE <- addMetadata(sprSE, list(targets), xName="metadata")
+```
+
+
+New Function:
+
+
+```r
+## Create empty SummarizedExperiment
+sprSE <- SPRdata()
+
+## Create an object with targets file and comparison and count table
+sprSE <- SPRdata(counts = countMatrix, cmp=TRUE, targetspath = targetspath)
+metadata(sprSE)
+colData(sprSE)
+assays(sprSE)
+```
+
+---
+## SPR Paper
+
+
+[Link to draft](https://www.overleaf.com/project/5e94948a23918a000116311c)
+
+
+Added the main points to discuss in the draft
+
+
+Writing: Results and introduction
+
+
+Improve Graphical Abstract
+
+
+Show case?
+
+---
+## *SYSargsList*
+
+
+Explain how *SYSargsList* is implemented - Vignette
+
+.small[
+| Function Name | Description |
+|----------------|-------------------------------------------------------------------------------------------|
+| `initWF` | Constructs `SYSargsList` workflow control module (S4 object) from script file |
+| `configWF` | Control of which step of the workflow will be run and the generation of the new RMarkdown |
+| `runWF` | Runs all the R chunk define in the RMarkdown file or a subset, e.g. `runWF[1:3]` |
+| `renderReport` | Render Scientific Report based on RMarkdown |
+| `renderLog` | Render logs Report based on RMarkdown |
+| `updateWF` | Recover the `SYSargsList` workflow previous ran and restarts the WF |
+| `plotWF` | Plot visual workflow designs and topologies with different graphical layouts |
+| `statusWF` | Return the overview of the workflow steps computational status |
+| `evalCode` | Turn eval option `TRUE` or `FALSE` on RMarkdown file |
+| `tryCL` | Checks if third-party software or utility is installed and set in the PATH |
+]
+
+
+Improve `statusWF()`
+
+---
+## Visualization in *systemPipeR*
+
+
+Add to vignette (SPR or SPS)
+ - `exploreDDS`, `exploreDDSplot`, `GLMplot`, `MAplot`, `MDSplot`, `PCAplot`, `hclustplot`, `heatMaplot`, `tSNEplot`, `volcanoplot`
+
+
+Enrichment analysis and visualization tool for SPR
+- Integration with `FGSEA`
+
+
+---
+## WebSite
+
+
+Updated the vignette
+
+
+Added *systemPipeRdata* vignette and presentation: [link](https://systempipe.org/docs/systemPipeRdata/)
+
+
+Redirect http://girke.bioinformatics.ucr.edu/systemPipeR/ to new page
+
+
+Add content to FAQ section
+
+
+Add tutorials videos
+
+---
+class: middle
+
+# Thanks!
+
+
+Browse source code at
+
+
+Ask a question about systemPipeR at Bioconductor Support Page
+
+
+
+*systemPipeRdata* at [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
+
+
+[https://systempipe.org/](https://systempipe.org/)
+
diff --git a/content/en/presentations/SPR/libs/tile-view/tile-view.js b/content/en/presentations/SPR/libs/tile-view/tile-view.js
index 7aac71611..bb31dc2fa 100644
--- a/content/en/presentations/SPR/libs/tile-view/tile-view.js
+++ b/content/en/presentations/SPR/libs/tile-view/tile-view.js
@@ -44,6 +44,10 @@
el.style.display = el.style.display === 'none' ? '' : 'none'
}
+ function slideshowResize () {
+ window.dispatchEvent(new Event('resize'))
+ }
+
const toggleTileView = function () {
toggleElement(tileView)
toggleElement(remarkSlideShow)
@@ -52,11 +56,8 @@
// tileView is now hidden, go to current slide
slideshow.gotoSlide(tileVars.currentSlideIdx + 1)
- // remove scroll/mousewheel event blocking
- tileView.removeEventListener('mousewheel', blockEvent)
- tileView.removeEventListener('DOMMouseScroll', blockEvent)
- console.log('removing blockScaling')
- document.removeEventListener('keydown', blockScaling)
+ slideshow.resume()
+ slideshowResize()
} else {
// store current slide index prior to launching tile-view
tileVars.currentSlideIdx = slideshow.getCurrentSlideIndex()
@@ -78,11 +79,7 @@
block: 'center'
})
- // block remarkjs from handling scroll events
- tileView.addEventListener('mousewheel', blockEvent)
- tileView.addEventListener('DOMMouseScroll', blockEvent)
- console.log('adding blockScaling')
- document.addEventListener('keydown', blockScaling)
+ slideshow.pause()
}
}
@@ -150,15 +147,6 @@
}
const tileVars = {}
- const blockEvent = ev => ev.stopPropagation()
- const blockScaling = function (ev) {
- if (ev.controlKey || ev.metaKey) {
- if (ev.key === '=' || ev.key === '-') {
- ev.preventDefault()
- console.log('window scaling is not allowed inside the tile overview')
- }
- }
- }
document.addEventListener('keydown', ev => {
if (ev.keyCode === launchKey) {
diff --git a/content/en/presentations/SPS/SPS_intro.knit.md b/content/en/presentations/SPS/SPS_intro.md
similarity index 100%
rename from content/en/presentations/SPS/SPS_intro.knit.md
rename to content/en/presentations/SPS/SPS_intro.md
diff --git a/content/en/sp/SPR/SP_docker.md b/content/en/sp/SPR/SP_docker.md
new file mode 100644
index 000000000..7513c10cb
--- /dev/null
+++ b/content/en/sp/SPR/SP_docker.md
@@ -0,0 +1,425 @@
+---
+title: "SPR Docker container"
+author: "Author: Daniela Cassol (danielac@ucr.edu)"
+date: "Last update: 25 April, 2021"
+output:
+ BiocStyle::html_document:
+ toc_float: true
+ code_folding: show
+ BiocStyle::pdf_document: default
+package: systemPipeR
+fontsize: 14pt
+type: docs
+weight: 8
+---
+
+> Guidelines from [bioconductor_docker](https://github.com/Bioconductor/bioconductor_docker).
+
+# Running the `systemPipeR` with Docker
+
+## Get a copy of the public docker image
+
+
+```bash
+docker pull systempipe/systempipe_docker:latest
+```
+
+## To run RStudio Server:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 \
+ systempipe/systempipe_docker:latest
+```
+
+You can then open a web browser pointing to your docker host on
+port 8787. If you're on Linux and using default settings, the docker
+host is `127.0.0.1` (or `localhost`, so the full URL to RStudio would
+be `http://localhost:8787)`. If you are on Mac or Windows and running
+`Docker Toolbox`, you can determine the docker host with the
+`docker-machine ip default` command.
+
+In the above command, `-e PASSWORD=` is setting the RStudio password
+and is required by the RStudio Docker image. It can be whatever you
+like except it cannot be `rstudio`. Log in to RStudio with the
+username `rstudio` and whatever password was specified, in this
+example `systemPipe`.
+
+## To run R from the command line:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest R
+```
+
+## To open a Bash shell on the container:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest bash
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+* * *
+
+
+# Install
+
+**Prerequisites**:
+[Linux](https://docs.docker.com/installation/)
+[Mac](http://docs.docker.com/installation/mac/)
+[Windows](http://docs.docker.com/installation/windows/)
+
+Instructions [here](https://docs.docker.com/engine/install/ubuntu/) on how to install Docker Engine on Ubuntu.
+
+
+```bash
+sudo apt-get update
+sudo apt-get install \
+ apt-transport-https \
+ ca-certificates \
+ curl \
+ gnupg
+curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+echo \
+ "deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
+ $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo apt-get update
+sudo apt-get install docker-ce docker-ce-cli containerd.io
+
+## Verify that Docker Engine is installed correctly by running the hello-world image.
+sudo docker run hello-world
+```
+
+## Uninstall
+
+
+```bash
+sudo apt-get remove docker docker-engine docker.io containerd runc
+```
+* * *
+
+
+# Docker Hub Account
+
+To be able to share a custom image, please go to https://hub.docker.com and
+create a free account.
+
+* * *
+
+
+## Log in to the Docker Hub locally
+
+Login with your Docker ID to push and pull images from Docker Hub. If you don't
+have a Docker ID, head over to https://hub.docker.com to create one.
+
+
+```bash
+docker login
+# Username: XXXX
+# Password: xxx
+# Login Succeeded
+```
+
+* * *
+
+
+# Run Docker
+
+
+```bash
+docker run-dP systempipe/systempipe_docker:latest
+```
+
+Make sure the container is running:
+
+```bash
+docker ps
+# CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS # NAMES
+#5d007f66a7b3 systempipe/systempipe_docker:latest "/init" 5 minutes ago Up 5 minutes 0.0.0.0:49153->8787/tcp determined_easle
+```
+
+## Login to the container
+
+Please check the `NAMES` in this example, `determined_easle,` to login into the container.
+
+
+```bash
+docker exec -it determined_easle /bin/bash
+```
+
+## Other alternatives to run the container
+
+### To run RStudio Server:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 \
+ systempipe/systempipe_docker:latest
+```
+
+### To run R from the command line:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest R
+```
+
+### To open a Bash shell on the container:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest bash
+```
+
+### Check R Version into the container
+
+
+```bash
+R --version
+```
+## Stop Docker
+
+
+```bash
+docker stop determined_easle
+```
+
+* * *
+
+
+# Create your first repository [Link](https://docs.docker.com/docker-hub/)
+
+## Create a repository:
+
+- Sign in to Docker Hub.
+- Click Create a Repository on the Docker Hub welcome page:
+- Name it /my-repo.
+- Click Create.
+
+## Build and push a container image to Docker Hub from your computer
+
+### Start by creating a *Dockerfile* to specify your application
+
+
+```bash
+mkdir docker_test
+cd docker_test
+touch Dockerfile
+```
+
+
+```bash
+# Docker inheritance
+FROM systempipe/systempipe_docker:latest
+
+## Install BiocStyle
+RUN R -e 'BiocManager::install("BiocStyle")'
+
+# Install required Bioconductor package from devel version
+RUN R -e 'BiocManager::install("tgirke/systemPipeR")'
+RUN R -e 'BiocManager::install("tgirke/systemPipeRdata")'
+
+WORKDIR /home/rstudio/SPRojects
+
+COPY --chown=rstudio:rstudio . /home/rstudio/SPRojects
+
+# Metadata
+LABEL name="systempipe/systempipe_docker" \
+ version=$BIOCONDUCTOR_DOCKER_systempipe \
+ url="https://github.com/systemPipeR/systempipe/systempipe_docker" \
+ vendor="systemPipeR Project" \
+ maintainer="email@gmail.com" \
+ description="Bioconductor docker image containing the systemPipeR Project" \
+ license="Artistic-2.0"
+```
+
+### Run `docker build` to build your Docker image
+
+
+```bash
+docker build -t systempipe/systempipe_docker .
+```
+
+### Run `docker run` to test your Docker image locally
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 systempipe/systempipe_docker:latest
+```
+
+### Run `docker push` to push your Docker image to Docker Hub
+
+
+```bash
+docker push systempipe/systempipe_docker
+```
+
+- Your repository in Docker Hub should now display a new latest tag under `Tags`
+
+* * *
+
+
+# Make changes to the container and Create the new image
+
+Create a folder, for example:
+
+```bash
+docker run -dP systempipe/systempipe_docker
+docker ps ## To check the NAME
+docker exec -it lucid_grothendieck /bin/bash
+root@33c758eb1626:/# R
+```
+
+
+```bash
+setwd("home/rstudio/")
+systemPipeRdata::genWorkenvir("rnaseq")
+```
+
+
+```bash
+exit
+docker commit -m "Added rnaseq template" -a "Dani Cassol" lucid_grothendieck dcassol/systempipeworkshop2021:rnaseq
+docker push systempipe/systempipe_docker:rnaseq
+```
+
+Run the new image:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 systempipe/systempipe_docker:rnaseq
+```
+
+* * *
+
+
+# Commands
+
+## List which docker machines are available locally
+```{bash, eval=FALSE}docker images```
+
+## List running containers
+```{bash, eval=FALSE}docker ps```
+
+## List all containers
+```{bash, eval=FALSE}docker ps -a```
+
+## Resume a stopped container
+```{bash, eval=FALSE}docker start ```
+
+## Shell into a running container
+```{bash, eval=FALSE}docker exec -it /bin/bash```
+
+## Stop OR remove a cointainer
+```{bash, eval=FALSE}docker stop ```
+```{bash, eval=FALSE}docker rm ```
+
+## Remove a image
+```{bash, eval=FALSE}docker rmi dcassol/systempipeworkshop2021:rnaseq```
+
+* * *
+
+
+# Docker and GitHub Actions
+
+1. To create a new token, go to Docker Hub Settings
+
+1.1. Account Settings >> Security >> New Access Token
+1.2. Add Access Token Description >> Create
+1.3. Copy the Access Token >> Copy and Close
+
+2. Go to the Repository at GitHub
+
+2.1. Settings > Secrets > New repository secret
+2.2. Create a new secret with the name `DOCKER_HUB_USERNAME` and your `Docker ID` as value
+2.3. Click at Add secret
+2.4. Create a new secret with the name `DOCKER_HUB_ACCESS_TOKEN` and your `Personal Access Token (PAT)` as value (generated in the previous step)
+
+3. Set up the GitHub Actions workflow
+
+
+```bash
+ steps:
+
+ - name: Checkout Repo
+ uses: actions/checkout@v2
+
+ - name: Login to Docker Hub
+ uses: docker/login-action@v1
+ with:
+ username: ${{ secrets.DOCKER_HUB_USERNAME }}
+ password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+```
+
+* * *
+
+
+
+# Common Problems
+
+
+```bash
+## Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.24/auth: dial unix /var/run/docker.sock: connect: permission denied
+```
+
+Solution:
+
+```bash
+sudo chmod 666 /var/run/docker.sock
+```
+
+* * *
+
+
+# Singularity Container
+
+Please download the Docker image of systemPipe, as follow:
+
+
+```bash
+singularity pull docker://systempipe/systempipe_docker:latest
+```
+
+You can also use the `build` command to download pre-built images from Docker.
+Unlike `pull`, `build` will convert the image to the latest Singularity image format after
+downloading it.
+
+
+```bash
+singularity build systempipe_docker_latest.sif docker://systempipe/systempipe_docker:latest
+```
+
+To run the container:
+
+
+```bash
+singularity shell systempipe_docker_latest.sif
+```
+
+* * *
+
+
+# Resources
+
+- [Docker Run: How to create images from an application](https://www.mirantis.com/blog/how-do-i-create-a-new-docker-image-for-my-application/)
+- [Docker Hub Quickstart](https://docs.docker.com/docker-hub/)
+- [Configure GitHub Actions](https://docs.docker.com/ci-cd/github-actions/)
+- [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#interact-with-images)
diff --git a/content/en/sps/_index.md b/content/en/sps/_index.md
index 5a92b38d1..12144dc38 100644
--- a/content/en/sps/_index.md
+++ b/content/en/sps/_index.md
@@ -82,6 +82,9 @@ For the login required demos, the app account name is **"user"** password **"use
For the admin panel login, account name **"admin"**, password **"admin"**.
+**Please DO NOT delete or change password when you are using the admin features.**
+_shinyapp.io_ will reset the app once a while, but this will affect other people
+who are trying the demo simultaneously.
## Other packages in systemPipeShiny
diff --git a/content/en/sps/adv_features/config.Rmd b/content/en/sps/adv_features/config.Rmd
index da22909e9..d9bb5fe6e 100644
--- a/content/en/sps/adv_features/config.Rmd
+++ b/content/en/sps/adv_features/config.Rmd
@@ -30,7 +30,6 @@ spsInit()
sps_dir <- normalizePath(".")
```
-
```{r echo=FALSE, results='asis'}
options(crayon.enabled = TRUE)
old_hooks <- fansi::set_knit_hooks(knitr::knit_hooks, which = c("output", "message", "error", "warning"))
@@ -131,7 +130,9 @@ options(sps = list(
module_wf = TRUE,
module_rnaseq = TRUE,
module_ggplot = TRUE,
- traceback = FALSE
+ traceback = FALSE,
+ is_demo = FALSE,
+ welcome_guide = TRUE
))
```
@@ -150,17 +151,19 @@ messages on console to tell you specifically what is wrong with your options.
PRE.fansi SPAN {padding-top: .25em; padding-bottom: .25em};
@@ -128,10 +127,10 @@ spsOptDefaults(app_path = sps_dir)
## Default: local
## Other: server
## login_screen:
-## Default: TRUE
-## Other: FALSE
+## Default: FALSE
+## Other: TRUE
## login_theme:
-## Default: vhelix
+## Default: random
## Other: *
## use_crayon:
## Default: TRUE
@@ -140,14 +139,14 @@ spsOptDefaults(app_path = sps_dir)
## Default: FALSE
## Other: TRUE
## admin_page:
-## Default: FALSE
-## Other: TRUE
+## Default: TRUE
+## Other: FALSE
## admin_url:
## Default: admin
## Other: *
## warning_toast:
-## Default: TRUE
-## Other: FALSE
+## Default: FALSE
+## Other: TRUE
## module_wf:
## Default: TRUE
## Other: FALSE
@@ -175,6 +174,12 @@ spsOptDefaults(app_path = sps_dir)
## traceback:
## Default: FALSE
## Other: TRUE
+## is_demo:
+## Default: FALSE
+## Other: TRUE
+## welcome_guide:
+## Default: TRUE
+## Other: FALSE
## * means any value will be accepted
@@ -186,10 +191,48 @@ spsOptions(app_path = sps_dir)
```
## Current project option settings:
-## verbose:
+## title:
+## systemPipeShiny
+## title_logo:
+## img/sps_small.png
+## mode:
+## local
+## login_screen:
## FALSE
+## login_theme:
+## random
## use_crayon:
## TRUE
+## verbose:
+## FALSE
+## admin_page:
+## TRUE
+## admin_url:
+## admin
+## warning_toast:
+## FALSE
+## module_wf:
+## TRUE
+## module_rnaseq:
+## TRUE
+## module_ggplot:
+## TRUE
+## tab_welcome:
+## TRUE
+## tab_vs_main:
+## TRUE
+## tab_canvas:
+## TRUE
+## tab_about:
+## TRUE
+## note_url:
+## https://raw.githubusercontent.com/systemPipeR/systemPipeShiny/master/inst/remote_resource/notifications.yaml
+## traceback:
+## FALSE
+## is_demo:
+## FALSE
+## welcome_guide:
+## TRUE
## ********
## Option legend:
## known options Hidden/custom options* and values+
@@ -220,7 +263,9 @@ options(sps = list(
module_wf = TRUE,
module_rnaseq = TRUE,
module_ggplot = TRUE,
- traceback = FALSE
+ traceback = FALSE,
+ is_demo = FALSE,
+ welcome_guide = TRUE
))
```
@@ -239,17 +284,19 @@ messages on console to tell you specifically what is wrong with your options.## title:
+## Default: systemPipeShiny
+## Other: *
+## title_logo:
+## Default: img/sps_small.png
+## Other: *
+## mode:
+## Default: local
+## Other: server
+## login_screen:
+## Default: FALSE
+## Other: TRUE
+## login_theme:
+## Default: random
+## Other: *
+## use_crayon:
+## Default: TRUE
+## Other: FALSE
+## verbose:
+## Default: FALSE
+## Other: TRUE
+## admin_page:
+## Default: TRUE
+## Other: FALSE
+## admin_url:
+## Default: admin
+## Other: *
+## warning_toast:
+## Default: FALSE
+## Other: TRUE
+## module_wf:
+## Default: TRUE
+## Other: FALSE
+## module_rnaseq:
+## Default: TRUE
+## Other: FALSE
+## module_ggplot:
+## Default: TRUE
+## Other: FALSE
+## tab_welcome:
+## Default: TRUE
+## Other: FALSE
+## tab_vs_main:
+## Default: TRUE
+## Other: FALSE
+## tab_canvas:
+## Default: TRUE
+## Other: FALSE
+## tab_about:
+## Default: TRUE
+## Other: FALSE
+## note_url:
+## Default: https://raw.githubusercontent.com/systemPipeR/systemPipeShiny/master/inst/remote_resource/notifications.yaml
+## Other: *
+## traceback:
+## Default: FALSE
+## Other: TRUE
+## is_demo:
+## Default: FALSE
+## Other: TRUE
+## welcome_guide:
+## Default: TRUE
+## Other: FALSE
+## my_opt1:
+## Default: TRUE
+## Other: FALSE
+## my_opt2:
+## Default: a
+## Other: *
+## * means any value will be accepted
+
+
+You can see the `my_opt1` and `my_opt2` have been added to SPS options.
+
+
+
+
+
+
+
+
+
+
+
diff --git a/content/en/sps/deploy.md b/content/en/sps/deploy.md
index bf92dd040..65f3aecd5 100644
--- a/content/en/sps/deploy.md
+++ b/content/en/sps/deploy.md
@@ -7,11 +7,101 @@ weight: 9
*****
## How to deploy the application
-Among several options of deployment of your `SPS` custom application, here you can find the example of [shinyapps.io](https://www.shinyapps.io/).
-To get started, it is required to create a *shinyapps.io* account. Please follow this [tutorial](https://shiny.rstudio.com/articles/shinyapps.html)
-with all the instructions to create an account.
-`SPS` project provides a ready-to-use file, `deploy.R`, with the required information to configure ShinyApps account and deploy the application.
-
-Once the account is set correctly, you can deploy it as soon as the project is created. It
-is recommended to create -> test/run -> deploy a Shiny app from Rstudio and follow
-[this tutorial](https://shiny.rstudio.com/articles/shinyapps.html).
+The easiest way to deploy SPS is [shinyapps.io{blk}](https://www.shinyapps.io/).
+To get started, it is required to create a *shinyapps.io* account. Please follow this [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html)
+with all the instructions to create an account. There are other ways to deploy, like
+AWS or Google Cloud with a custom Shiny server. There are a lot of tutorials to
+deploy the app other than *shinyapps.io*. We only use *shinyapps.io* as the example
+here to discuss how to deploy.
+
+## Get started
+
+After you have created a `SPS` project, it is in a deploy-ready state, which means
+you can deploy it as soon as you create the project.
+
+We have created some important helper code in `deploy.R` under the project root for you.
+1. Read the [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html)
+2. After you have the accounts and token set up according to the tutorial, open
+ `deploy.R`.
+ - If you have used Bioconductor packages (mostly likely yes, unless you do not use
+ the default modules), run the options line in R console before deploy, which is this
+
+ ```r
+ options(repos = BiocManager::repositories())
+ ```
+
+ - If you want to use develop version of Bioconductor packages (not recommended),
+ uncomment following lines and follow the instructions in the file.
+
+ ```r
+ # repos <- BiocManager::repositories()
+ # devel <- "3.13"
+ # repos[length(repos) + 1] <- paste0("https://bioconductor.org/packages/", devel, "/bioc")
+ # names(repos)[length(repos)] <- "BioC"
+ # options(repos = repos)
+ # getOption("repos")
+ ```
+
+ - If you wish *shinyapps.io* to install [SPS modules](/sps/modules/), copy and
+ **uncomment** following lines for the modules to `global.R` file below the
+ line `# load additional libraries that you want to use below`.
+ ```r
+ ## Workflow module
+ # requireNamespace("DOT"); requireNamespace("networkD3"); requireNamespace("pushbar")
+ # requireNamespace("readr"); requireNamespace("rhandsontable"); requireNamespace("shinyTree")
+ # requireNamespace("systemPipeR"); requireNamespace("systemPipeRdata"); requireNamespace("zip")
+
+ ## RNA-Seq module
+ # requireNamespace("DESeq2"); requireNamespace("Rtsne"); requireNamespace("SummarizedExperiment")
+ # requireNamespace("UpSetR"); requireNamespace("ape"); requireNamespace("ggtree")
+ # requireNamespace("glmpca"); requireNamespace("pheatmap"); requireNamespace("systemPipeR")
+
+ ## Quick ggplot module
+ # requireNamespace("esquisse")
+ ```
+ - The last section in `deploy.R` is some helper code to set up the account and
+ deploy the app programmatically. If you use the
+ [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html),
+ there is no need to do this section.
+ - Save your changes in the `global.R`.
+
+## Deploy in Rstudio
+We recommend you to deploy the app with Rstudio. If you have set up your *shinyapps.io*
+account, we are ready to go.
+
+
+
+
+
+
+
+### A
+1. Open `global.R` in Rstudio, use the "Run App" button to make sure your app
+can be run without problems locally.
+2. Run `options(repos = BiocManager::repositories())` and other Bioconductor
+ set up code as listed above.
+3. Click the button next to "Run App" and choose "Publish Application..."
+
+### B
+4. If you have set up your account correctly, you should see your account to the
+ right panel.
+5. Select all the files of your SPS project.
+6. Change the app "Title" to what you want.
+7. hit "Publish".
+
+## RAM requirement
+
+If you wish to load the workflow and/or RNAseq module(s) on *shinyapps.io*, you need
+at least **2GB** of memory. Unfortunately, these 2 modules depend heavily on Bioconductor
+packages and these packages are not light-weighted. The max RAM for free account
+on *shinyapps.io* is 1GB which means you either need to upgrade your account or
+use other server to deploy your app.
+
+If you decide to not load these modules which will allow you to deploy the app
+with a free account, change the settings to unload these modules in
+[app options](/sps/adv_features/config/#app-options) in `global.R`.
+
+
+
+
+
diff --git a/content/en/sps/img/deploy.png b/content/en/sps/img/deploy.png
new file mode 100644
index 000000000..e1daafda5
Binary files /dev/null and b/content/en/sps/img/deploy.png differ
diff --git a/content/en/sps/modules/workflow.md b/content/en/sps/modules/workflow.md
index b2ecadfb6..2438d9c9c 100644
--- a/content/en/sps/modules/workflow.md
+++ b/content/en/sps/modules/workflow.md
@@ -9,12 +9,12 @@ weight: 1
The workflow management module in `SPS` allows one to modify or create the
configuration files required for running data analysis workflows in
-[systemPipeR](https://systempipe.org/docs/systemPipeR/) (SPR). This includes
+[systemPipeR](https://systempipe.org/sp/spr/) (SPR). This includes
three types of important files: a sample metadata (targets) file, a
workflow file (in R Markdown format) defining the workflow steps, and workflow running
-files in [Common Workflow Language (CWL)](https://www.commonwl.org/) format. In SPS, one can easily create
+files in [Common Workflow Language (CWL){blk}](https://www.commonwl.org/) format. In SPS, one can easily create
these files under the "Workflow Management" module, located in navigation bar
-on the left of the dashboard ([Fig2](/sps/quick_start/#launch-sps)).
+on the [left of the dashboard](/sps/quick_start/#launch-sps).
The current version of `SPS` allows to:
@@ -43,13 +43,13 @@ sequencing workflows.
Clicking the pop-up will jump you to the step 2. The status tracker and banner for
step 1 should all turn green.
-
### 2. Prepare a target file
+
The targets file defines all input file paths and other sample information of
analysis workflows. To better undertand the structure of this file, one can
consult the ["Structure of targets
-file"](https://systempipe.org/docs/systemPipeR/#structure-of-targets-file)
+file"](https://systempipe.org/sp/spr/gettingstarted/#structure-of-targets-file)
section in the SPR vignette. Essentially, this is the tabular file representation
of the `colData` slot in an `SummarizedExperiment` object which stores sample
IDs and other meta information.
@@ -75,7 +75,7 @@ here. Leave it as default for other projects.
### 3. Prepare a workflow file
-In SPR, workflows are defined in Rmarkdown files, you can read details and obtain them [here](https://systempipe.org/pages/pipelines_area/).
+In SPR, workflows are defined in Rmarkdown files, you can read details and obtain them [here](https://systempipe.org/sp/spr/templates/).
Now let us follow the order below to see how SPS helps you to prepare a workflow file for a RNAseq project (Fig.3 B):
@@ -152,3 +152,33 @@ code.
5. Workflow running log.
6. View any plot output. and send a copy of your current plot to SPS Canvas tab or
download it.
+
+
+## App security
+Running the workflow may introduce some security concerns. Read [App Security](/sps/adv_features/app_security/#the-workflow-module)
+for more details.
+
+## `is_demo` option
+The `is_demo` [option](/sps/adv_features/config/#app-options) will impact the workflow
+module.
+- `TRUE`: you are not deploying the app for production purpose. It is just a show case.
+ Under this option, users who are trying to create a workflow will be locked inside
+ a temp directory and every time they start a new session, they will be assigned to
+ a new temp directory. This is useful is many people want to try the app the same
+ time, so they will have private different environment, and the temp directory will
+ be removed afterwards.
+- `FALSE`: you are using the app on your own local computer or use it in a production
+ environment. WF module will have **full access** to the sever storage system and
+ users can choose **any place** they have permission to create the workflow session.
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/content/en/training/Presentations/_index.md b/content/en/training/Presentations/_index.md
index 4a94b7c9e..2705940bd 100644
--- a/content/en/training/Presentations/_index.md
+++ b/content/en/training/Presentations/_index.md
@@ -11,7 +11,7 @@ type: docs
-## [systemPipeRdata{blk}](http://bioconductor.org/packages/devel/bioc/html/systemPipeShiny.html)
+## [systemPipeShiny{blk}](http://bioconductor.org/packages/devel/bioc/html/systemPipeShiny.html)
diff --git a/public/404.html b/public/404.html
index 24c7408ba..234d59108 100644
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@@ -45,8 +45,8 @@
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+
Daniela Cassol" +institute: "
University of California Riverside"
+date: "2020/10/20 (updated: 2021-04-25)"
+output:
+ xaringan::moon_reader:
+ css: ["css/xaringan-themer.css", "css/custom.css"]
+ lib_dir: libs
+ nature:
+ highlightStyle: github
+ highlightLines: true
+ countIncrementalSlides: true
+ # seal: false
+---
+
+layout: true
+background-image: url(https://raw.githubusercontent.com/tgirke/systemPipeR/gh-pages/images/systemPipeR.png)
+background-position: 99% 1%
+background-size: 10%
+
+
+
+
+
+
+
+---
+class: middle
+
+## Outline
+
+#### Introduction
+#### Design
+#### How to run a Workflow
+#### Workflows Tutorial
+#### Live Demo
+
+
+
+
+---
+class: inverse, center, middle
+
+# Introduction
+
+
+---
+## Introduction
+
+
+[_systemPipeR_](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html) provides a suite of R/Bioconductor packages for designing, building and running end-to-end analysis workflows on local machines, HPC clusters and cloud systems, while generating at the same time publication quality analysis reports
+
+
+_systemPipeR_ offers many utilities to build, control, and execute
+workflows entirely from R
+
+
+The environment takes advantage of central community S4 classes of the Bioconductor ecosystem
+
+
+Workflows are managed by generic workflow management containers supporting both analysis routines implemented in R code and/or command-line software
+
+
+Simple annotation system targets
+
+
+---
+### systemPipeR’s Core Functionalities
+
+.center[
+
+]
+
+
+
+---
+## Structural Features
+
+--
+.left-column[
+#### WF infrastructure
+]
+
+.right-column[
+*systemPipeR* offers many utilities to build, control, and execute
+workflows entirely from R. The environment takes advantage of central community S4 classes
+of the Bioconductor ecosystem. Workflows are managed by generic workflow management
+containers supporting both analysis routines implemented in R code and/or command-line
+software. A layered monitoring infrastructure is provided to design, control and debug each
+step in a workflow. The run environment allows to execute workflows entirely or with a
+intuitive to use step-wise execution syntax using R’s standard subsetting syntax
+(runWF(sys[1:3])) or pipes (%>%).
+]
+
+---
+
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+]
+
+.right-column[
+An important feature of systemPipeR is support for
+running command-line software by adopting the Common Workflow Language (CWL). The
+latter is a widely adopted community standard for describing analysis workflows. This design
+offers several advantages such as:
+
+
+seamless integration of most command-line software
+
+
+support to run systemPipeR workflows from R or many other popular computer languages
+
+
+efficient sharing of workflows across different workflow environments.
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+]
+
+.right-column[
+The processing time of workflows can be greatly reduced by making use
+of parallel evaluations across several CPU cores on single machines, or multiple nodes of
+computer clusters and cloud-based systems. systemPipeR simplifies these parallelization tasks
+without creating any limitations for users who do not have access to high-performance
+computer resources
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+]
+
+.right-column[
+*systemPipeR’s* reporting infrastructure
+includes three types of interconnected reports each serving a different purpose:
+
+
+a scientific report, based on R Markdown, contains all scientifically relevant results
+
+
+a technical report captures all technical information important for each workflow step, including parameter
+settings, software versions, and warning/error messages, etc.
+
+
+a visual report depicts the entire workflow topology including its run status in form of a workflow graph
+
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+#### Shiny Web Interface
+]
+
+.right-column[
+Recently, the systemPipeShiny package has been added that allows
+users to design workflows in an interactive graphical user interface (GUI). In addition to
+designing workflows, this new interface allows users to run and to monitor workflows in an
+intuitive manner without the need of knowing R.
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+#### Shiny Web Interface
+#### Workflow Templates
+]
+
+.right-column[
+A rich set of end-to-end workflow templates is provided by this
+project for a wide range omics applications. In addition, users can contribute and share their
+workflows with the community by submitting them to a central GitHub repository
+]
+
+
+---
+## Important Functions
+
+.small[
+| Function Name | Description | Category |
+|-------------------|-----------------------------------------------------------------------------------------------------------------------|-----------------|
+| `genWorkenvir` | Generates workflow templates provided by systemPipeRdata helper package / or from the individuals’ pipelines packages | Accessory |
+| `loadWorkflow` | Constructs `SYSargs2` object from CWL param and targets files | ``SYSargs2`` |
+| `renderWF` | Populate all the command-line in an `SYSargs2` object | ``SYSargs2`` |
+| `subsetWF` | Subsetting `SYSargs2` class slots | ``SYSargs2`` |
+| `runCommandline` | Executes command-line software on samples and parameters specified in `SYSargs2` object | ``SYSargs2`` |
+| `clusterRun` | Runs command-line software in parallel mode on a computer cluster | ``SYSargs2`` |
+| `writeTargetsout` | Write updated targets out to file/Generate targets file with reference | ``SYSargs2`` |
+| `output_update` | Updates the output files paths in the `SYSargs2` object | ``SYSargs2`` |
+| `singleYML` | Create automatically the `param.yml` | ``SYSargs2`` |
+| `createWF` | Create automatically `param.cwl` and the `param.yml` based on the command line | ``SYSargs2`` |
+| `config.param` | Custom configuration of the CWL param files from R | ``SYSargs2`` |
+]
+
+---
+## Important Functions
+
+.small[
+| Function Name | Description | Category |
+|-------------------|-----------------------------------------------------------------------------------------------------------------------|-----------------|
+| `initWF` | Constructs `SYSargsList` workflow control module (S4 object) from script file | ``SYSargsList`` |
+| `configWF` | Control of which step of the workflow will be run and the generation of the new RMarkdown | ``SYSargsList`` |
+| `runWF` | Runs all the R chunk define in the RMarkdown file or a subset, e.g. `runWF[1:3]` | ``SYSargsList`` |
+| `renderReport` | Render Scientific Report based on RMarkdown | ``SYSargsList`` |
+| `subsetRmd` | Write updated subset Rmarkdown of R chunk with text associate in the step selected | ``SYSargsList`` |
+| `plotWF` | Plot visual workflow designs and topologies with different graphical layouts | ``SYSargsList`` |
+| `statusWF` | Return the overview of the workflow steps computational status | ``SYSargsList`` |
+| `evalCode` | Turn eval option `TRUE` or `FALSE` on RMarkdown file | Accessory |
+| `tryCL` | Checks if third-party software or utility is installed and set in the PATH | Accessory |
+]
+
+
+
+
+
+
+---
+class: inverse, center, middle
+
+# Design
+
+---
+### Workflow Management Solutions
+
+
+*systemPipeR* central concept for designing workflows is **workflow
+management containers** (S4 class)
+
+
+*SYSargs2* controls workflow steps with input/output file operations
+
+
+*SYSargs2* requires a targets and a set of workflow definition files (here param.cwl and param.yml)
+
+
+
+
+
+*SYSargsList* objects organize one or many *SYSargs2*
+containers in a single compound object capturing all information required to run, control and
+monitor complex workflows from start to finish
+
+.center[
+
+]
+
+---
+## 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 | |  |
+| [systemPipeRIBOseq](https://systempiper.github.io/systemPipeRIBOseq/articles/systemPipeRIBOseq.html) | RIBO-Seq Workflow Template | v1.0 | |  |
+| [systemPipeRNAseq](https://systempiper.github.io/systemPipeRNAseq/articles/systemPipeRNAseq.html) | RNA-Seq Workflow Template | v1.0 | |  |
+| [systemPipeVARseq](https://systempiper.github.io/systemPipeVARseq/articles/systemPipeVARseq.html) | VAR-Seq Workflow Template | v1.0 | |  |
+| [systemPipeMethylseq](https://github.com/systemPipeR/systemPipeMethylseq) | Methyl-Seq Workflow Template | devel | |  |
+| [systemPipeDeNovo](https://github.com/systemPipeR/systemPipeDeNovo) | De novo transcriptome assembly Workflow Template | devel | |  |
+| [systemPipeCLIPseq](https://github.com/systemPipeR/systemPipeCLIPseq) | CLIP-Seq Workflow Template | devel | |  |
+| [systemPipeMetaTrans](https://github.com/systemPipeR/systemPipeMetaTrans) | Metatranscriptomic Sequencing Workflow Template | devel | |  |
+]
+
+---
+class: inverse, center, middle
+
+# CWL
+
+---
+## CWL
+
+ **TODO:**
+Add section with CWL details
+
+.center[
+
+]
+
+---
+## CWL and SPR
+
+ **TODO:**
+How to use CWL definition with *systemPipeR*
+
+- *SYSargs2* instances are constructed from a *`targets`* file and two *`param`* file
+ - *`hisat2-mapping-se.cwl`* file contains the settings for running command-line software
+ - *`hisat2-mapping-se.yml`* file define all the variables to be input in the specific command-line step
+
+
+```r
+targets <- system.file("extdata", "targets.txt", package="systemPipeR")
+dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
+align <- loadWF(targets=targets, wf_file="hisat2-mapping-se.cwl",
+ input_file="hisat2-mapping-se.yml", dir_path=dir_path)
+align <- renderWF(align, inputvars=c(FileName="_FASTQ_PATH_", SampleName="_SampleName_"))
+
+## Instance of 'SYSargs2':
+## Slot names/accessors:
+## targets: 18 (M1A...V12B), targetsheader: 4 (lines)
+## modules: 2
+## wf: 0, clt: 1, yamlinput: 7 (components)
+## input: 18, output: 18
+## cmdlist: 18
+## WF Steps:
+## 1. hisat2-mapping-se.cwl (rendered: TRUE)
+```
+
+---
+## CWL and SPR
+
+## *`SYSargs2`* instance
+
+- Slots and accessor functions have the same names
+
+```r
+names(align)
+# [1] "targets" "targetsheader" "modules" "wf" "clt"
+# [6] "yamlinput" "cmdlist" "input" "output" "cwlfiles"
+# [11] "inputvars"
+```
+
+- *`cmdlist`* return command-line arguments for the specific software, here *`HISAT2`* for the first sample
+
+```r
+cmdlist(align)[1]
+# $M1A
+# $M1A$`hisat2-mapping-se.cwl`
+# [1] "hisat2 -S results/M1A.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446027_1.fastq.gz --threads 4"
+```
+
+- The output components of *`SYSargs2`* define all the expected output files for each step in the workflow; some of which are the input for the next workflow step
+
+
+```r
+output(align)[1]
+# $M1A
+# $M1A$`hisat2-mapping-se.cwl`
+# [1] "results/M1A.sam"
+```
+
+---
+class: inverse, center, middle
+
+# Metadata
+
+---
+### *Targets* file organizes samples
+
+- Structure of *`targets`* file for single-end (SE) library
+
+```r
+targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:3,1:4]
+```
+
+```
+## FileName SampleName Factor SampleLong
+## 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A
+## 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B
+## 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A
+```
+
+- Structure of *`targets`* file for paired-end (PE) library
+
+```r
+targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:3,1:5]
+```
+
+```
+## FileName1 FileName2 SampleName Factor
+## 1 ./data/SRR446027_1.fastq.gz ./data/SRR446027_2.fastq.gz M1A M1
+## 2 ./data/SRR446028_1.fastq.gz ./data/SRR446028_2.fastq.gz M1B M1
+## 3 ./data/SRR446029_1.fastq.gz ./data/SRR446029_2.fastq.gz A1A A1
+## SampleLong
+## 1 Mock.1h.A
+## 2 Mock.1h.B
+## 3 Avr.1h.A
+```
+
+---
+### Integration with *SummarizedExperiment*
+
+- Integrates *targets* files and count table from *systemPipeR* to a *SummarizedExperiment* object
+
+
+```r
+## Create an object with targets file and comparison and count table
+sprSE <- SPRdata(targetspath = targetspath, cmp=TRUE)
+metadata(sprSE)
+# $version
+# [1] ‘1.23.9’
+#
+# $comparison
+# $comparison$CMPset1
+# [,1] [,2]
+# [1,] "M1" "A1"
+# [2,] "M1" "V1"
+# [3,] "A1" "V1"
+# [4,] "M6" "A6"
+
+colData(sprSE)
+# DataFrame with 18 rows and 6 columns
+# FileName SampleName Factor SampleLong
+#
+# M1A ./data/SRR446027_1.f.. M1A M1 Mock.1h.A
+# M1B ./data/SRR446028_1.f.. M1B M1 Mock.1h.B
+# ... ... ... ... ...
+# M12B ./data/SRR446040_1.f.. M12B M12 Mock.12h.B
+```
+
+---
+class: inverse, center, middle
+
+# 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("systemPipeR")
+```
+
+### Load Package and Documentation
+
+
+Load package:
+
+
+```r
+library("systemPipeR")
+```
+
+
+Access help:
+
+
+```r
+library(help="systemPipeR")
+vignette("systemPipeR")
+```
+
+---
+## Quick Start
+
+### Load Sample Workflow
+
+
+*systemPipeRdata*
+
+- Helper package to generate with a single command workflow templates for *systemPipeR*
+- Includes sample data for testing
+- User can create new workflows or change and extend existing ones
+- Template Workflows:
+ - Sample workflows can be loaded with the *`genWorkenvir`* function from **systemPipeRdata**
+
+
+Generate workflow template:
+
+
+```r
+library(systemPipeRdata)
+genWorkenvir(workflow="rnaseq")
+setwd("rnaseq")
+```
+
+
+More details about *systemPipeRdata* package [here](https://systempipe.org/pages/SPRdata_intro/SPRdata_intro#1)
+
+---
+## 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
+```
+
+---
+## Dynamic Workflow Template
+
+
+Create dynamic Workflow Templates with *RStudio*
+
+
+`File -> New File -> R Markdown -> From Template`
+.center[
+
+]
+
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+]
+
+.right-column[
+
+```r
+library(systemPipeR)
+targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:4,1:4]
+```
+
+```
+## FileName SampleName Factor SampleLong
+## 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A
+## 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B
+## 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A
+## 4 ./data/SRR446030_1.fastq.gz A1B A1 Avr.1h.B
+```
+
+```r
+script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- initWF(script = script, targets = targetspath, overwrite = TRUE)
+# Project started with success: ./SYSproject and SYSconfig.yml were created.
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- configWF(sysargslist, input_steps = "1:3")
+sysargslist
+# Instance of 'SYSargsList':
+# WF Steps:
+# 1. Rmarkdown/HTML setting
+# 2. Introduction
+# 3. Samples and environment settings
+# 3.1. Environment settings and input data
+# 3.2. Required packages and resources
+# 3.3. Experiment definition provided by `targets` file
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+### `runWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- runWF(sysargslist, steps = "1:2")
+# Step: 1: Introduction --> DONE
+# Step: 2: Samples and environment settings --> DONE
+# Step: 2.1: Environment settings and input data --> DONE
+# Step: 2.2: Required packages and resources --> DONE
+# Step: 2.3: Experiment definition provided by `targets` file --> DONE
+```
+
+
+```r
+sysargslist <- runWF(sysargslist, steps = "ALL")
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+### `runWF`
+### `renderReport`
+]
+
+.right-column[
+
+```r
+sysargslist <- renderReport(sysargslist = sysargslist)
+```
+]
+
+---
+## How to Use Pipes `%>%`
+
+Consider the following example, in which the steps are the initialization, configuration and running the entire workflow.
+
+
+```r
+library(systemPipeR)
+sysargslist <- initWF(script ="systemPipeRNAseq.Rmd", overwrite = TRUE) %>%
+ configWF(input_steps = "1:6") %>%
+ runWF(steps = "1:2")
+```
+
+---
+class: inverse, center, middle
+
+# Project Updates
+
+---
+### *targets* x *SummarizedExperiment*
+
+Extension "SummarizedExperiment" methods:
+
+
+```r
+sprSE <- addAssay(sprSE, assay(countMatrix), xName="countMatrix")
+sprSE <- addMetadata(sprSE, list(targets), xName="metadata")
+```
+
+
+New Function:
+
+
+```r
+## Create empty SummarizedExperiment
+sprSE <- SPRdata()
+
+## Create an object with targets file and comparison and count table
+sprSE <- SPRdata(counts = countMatrix, cmp=TRUE, targetspath = targetspath)
+metadata(sprSE)
+colData(sprSE)
+assays(sprSE)
+```
+
+---
+## SPR Paper
+
+
+[Link to draft](https://www.overleaf.com/project/5e94948a23918a000116311c)
+
+
+Added the main points to discuss in the draft
+
+
+Writing: Results and introduction
+
+
+Improve Graphical Abstract
+
+
+Show case?
+
+---
+## *SYSargsList*
+
+
+Explain how *SYSargsList* is implemented - Vignette
+
+.small[
+| Function Name | Description |
+|----------------|-------------------------------------------------------------------------------------------|
+| `initWF` | Constructs `SYSargsList` workflow control module (S4 object) from script file |
+| `configWF` | Control of which step of the workflow will be run and the generation of the new RMarkdown |
+| `runWF` | Runs all the R chunk define in the RMarkdown file or a subset, e.g. `runWF[1:3]` |
+| `renderReport` | Render Scientific Report based on RMarkdown |
+| `renderLog` | Render logs Report based on RMarkdown |
+| `updateWF` | Recover the `SYSargsList` workflow previous ran and restarts the WF |
+| `plotWF` | Plot visual workflow designs and topologies with different graphical layouts |
+| `statusWF` | Return the overview of the workflow steps computational status |
+| `evalCode` | Turn eval option `TRUE` or `FALSE` on RMarkdown file |
+| `tryCL` | Checks if third-party software or utility is installed and set in the PATH |
+]
+
+
+Improve `statusWF()`
+
+---
+## Visualization in *systemPipeR*
+
+
+Add to vignette (SPR or SPS)
+ - `exploreDDS`, `exploreDDSplot`, `GLMplot`, `MAplot`, `MDSplot`, `PCAplot`, `hclustplot`, `heatMaplot`, `tSNEplot`, `volcanoplot`
+
+
+Enrichment analysis and visualization tool for SPR
+- Integration with `FGSEA`
+
+
+---
+## WebSite
+
+
+Updated the vignette
+
+
+Added *systemPipeRdata* vignette and presentation: [link](https://systempipe.org/docs/systemPipeRdata/)
+
+
+Redirect http://girke.bioinformatics.ucr.edu/systemPipeR/ to new page
+
+
+Add content to FAQ section
+
+
+Add tutorials videos
+
+---
+class: middle
+
+# Thanks!
+
+
+Browse source code at
+
+
+Ask a question about systemPipeR at Bioconductor Support Page
+
+
+
+*systemPipeRdata* at [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
+
+
+[https://systempipe.org/](https://systempipe.org/)
+
diff --git a/content/en/presentations/SPR/libs/tile-view/tile-view.js b/content/en/presentations/SPR/libs/tile-view/tile-view.js
index 7aac71611..bb31dc2fa 100644
--- a/content/en/presentations/SPR/libs/tile-view/tile-view.js
+++ b/content/en/presentations/SPR/libs/tile-view/tile-view.js
@@ -44,6 +44,10 @@
el.style.display = el.style.display === 'none' ? '' : 'none'
}
+ function slideshowResize () {
+ window.dispatchEvent(new Event('resize'))
+ }
+
const toggleTileView = function () {
toggleElement(tileView)
toggleElement(remarkSlideShow)
@@ -52,11 +56,8 @@
// tileView is now hidden, go to current slide
slideshow.gotoSlide(tileVars.currentSlideIdx + 1)
- // remove scroll/mousewheel event blocking
- tileView.removeEventListener('mousewheel', blockEvent)
- tileView.removeEventListener('DOMMouseScroll', blockEvent)
- console.log('removing blockScaling')
- document.removeEventListener('keydown', blockScaling)
+ slideshow.resume()
+ slideshowResize()
} else {
// store current slide index prior to launching tile-view
tileVars.currentSlideIdx = slideshow.getCurrentSlideIndex()
@@ -78,11 +79,7 @@
block: 'center'
})
- // block remarkjs from handling scroll events
- tileView.addEventListener('mousewheel', blockEvent)
- tileView.addEventListener('DOMMouseScroll', blockEvent)
- console.log('adding blockScaling')
- document.addEventListener('keydown', blockScaling)
+ slideshow.pause()
}
}
@@ -150,15 +147,6 @@
}
const tileVars = {}
- const blockEvent = ev => ev.stopPropagation()
- const blockScaling = function (ev) {
- if (ev.controlKey || ev.metaKey) {
- if (ev.key === '=' || ev.key === '-') {
- ev.preventDefault()
- console.log('window scaling is not allowed inside the tile overview')
- }
- }
- }
document.addEventListener('keydown', ev => {
if (ev.keyCode === launchKey) {
diff --git a/content/en/presentations/SPS/SPS_intro.knit.md b/content/en/presentations/SPS/SPS_intro.md
similarity index 100%
rename from content/en/presentations/SPS/SPS_intro.knit.md
rename to content/en/presentations/SPS/SPS_intro.md
diff --git a/content/en/sp/SPR/SP_docker.md b/content/en/sp/SPR/SP_docker.md
new file mode 100644
index 000000000..7513c10cb
--- /dev/null
+++ b/content/en/sp/SPR/SP_docker.md
@@ -0,0 +1,425 @@
+---
+title: "SPR Docker container"
+author: "Author: Daniela Cassol (danielac@ucr.edu)"
+date: "Last update: 25 April, 2021"
+output:
+ BiocStyle::html_document:
+ toc_float: true
+ code_folding: show
+ BiocStyle::pdf_document: default
+package: systemPipeR
+fontsize: 14pt
+type: docs
+weight: 8
+---
+
+> Guidelines from [bioconductor_docker](https://github.com/Bioconductor/bioconductor_docker).
+
+# Running the `systemPipeR` with Docker
+
+## Get a copy of the public docker image
+
+
+```bash
+docker pull systempipe/systempipe_docker:latest
+```
+
+## To run RStudio Server:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 \
+ systempipe/systempipe_docker:latest
+```
+
+You can then open a web browser pointing to your docker host on
+port 8787. If you're on Linux and using default settings, the docker
+host is `127.0.0.1` (or `localhost`, so the full URL to RStudio would
+be `http://localhost:8787)`. If you are on Mac or Windows and running
+`Docker Toolbox`, you can determine the docker host with the
+`docker-machine ip default` command.
+
+In the above command, `-e PASSWORD=` is setting the RStudio password
+and is required by the RStudio Docker image. It can be whatever you
+like except it cannot be `rstudio`. Log in to RStudio with the
+username `rstudio` and whatever password was specified, in this
+example `systemPipe`.
+
+## To run R from the command line:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest R
+```
+
+## To open a Bash shell on the container:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest bash
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+* * *
+
+
+# Install
+
+**Prerequisites**:
+[Linux](https://docs.docker.com/installation/)
+[Mac](http://docs.docker.com/installation/mac/)
+[Windows](http://docs.docker.com/installation/windows/)
+
+Instructions [here](https://docs.docker.com/engine/install/ubuntu/) on how to install Docker Engine on Ubuntu.
+
+
+```bash
+sudo apt-get update
+sudo apt-get install \
+ apt-transport-https \
+ ca-certificates \
+ curl \
+ gnupg
+curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+echo \
+ "deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
+ $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo apt-get update
+sudo apt-get install docker-ce docker-ce-cli containerd.io
+
+## Verify that Docker Engine is installed correctly by running the hello-world image.
+sudo docker run hello-world
+```
+
+## Uninstall
+
+
+```bash
+sudo apt-get remove docker docker-engine docker.io containerd runc
+```
+* * *
+
+
+# Docker Hub Account
+
+To be able to share a custom image, please go to https://hub.docker.com and
+create a free account.
+
+* * *
+
+
+## Log in to the Docker Hub locally
+
+Login with your Docker ID to push and pull images from Docker Hub. If you don't
+have a Docker ID, head over to https://hub.docker.com to create one.
+
+
+```bash
+docker login
+# Username: XXXX
+# Password: xxx
+# Login Succeeded
+```
+
+* * *
+
+
+# Run Docker
+
+
+```bash
+docker run-dP systempipe/systempipe_docker:latest
+```
+
+Make sure the container is running:
+
+```bash
+docker ps
+# CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS # NAMES
+#5d007f66a7b3 systempipe/systempipe_docker:latest "/init" 5 minutes ago Up 5 minutes 0.0.0.0:49153->8787/tcp determined_easle
+```
+
+## Login to the container
+
+Please check the `NAMES` in this example, `determined_easle,` to login into the container.
+
+
+```bash
+docker exec -it determined_easle /bin/bash
+```
+
+## Other alternatives to run the container
+
+### To run RStudio Server:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 \
+ systempipe/systempipe_docker:latest
+```
+
+### To run R from the command line:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest R
+```
+
+### To open a Bash shell on the container:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest bash
+```
+
+### Check R Version into the container
+
+
+```bash
+R --version
+```
+## Stop Docker
+
+
+```bash
+docker stop determined_easle
+```
+
+* * *
+
+
+# Create your first repository [Link](https://docs.docker.com/docker-hub/)
+
+## Create a repository:
+
+- Sign in to Docker Hub.
+- Click Create a Repository on the Docker Hub welcome page:
+- Name it /my-repo.
+- Click Create.
+
+## Build and push a container image to Docker Hub from your computer
+
+### Start by creating a *Dockerfile* to specify your application
+
+
+```bash
+mkdir docker_test
+cd docker_test
+touch Dockerfile
+```
+
+
+```bash
+# Docker inheritance
+FROM systempipe/systempipe_docker:latest
+
+## Install BiocStyle
+RUN R -e 'BiocManager::install("BiocStyle")'
+
+# Install required Bioconductor package from devel version
+RUN R -e 'BiocManager::install("tgirke/systemPipeR")'
+RUN R -e 'BiocManager::install("tgirke/systemPipeRdata")'
+
+WORKDIR /home/rstudio/SPRojects
+
+COPY --chown=rstudio:rstudio . /home/rstudio/SPRojects
+
+# Metadata
+LABEL name="systempipe/systempipe_docker" \
+ version=$BIOCONDUCTOR_DOCKER_systempipe \
+ url="https://github.com/systemPipeR/systempipe/systempipe_docker" \
+ vendor="systemPipeR Project" \
+ maintainer="email@gmail.com" \
+ description="Bioconductor docker image containing the systemPipeR Project" \
+ license="Artistic-2.0"
+```
+
+### Run `docker build` to build your Docker image
+
+
+```bash
+docker build -t systempipe/systempipe_docker .
+```
+
+### Run `docker run` to test your Docker image locally
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 systempipe/systempipe_docker:latest
+```
+
+### Run `docker push` to push your Docker image to Docker Hub
+
+
+```bash
+docker push systempipe/systempipe_docker
+```
+
+- Your repository in Docker Hub should now display a new latest tag under `Tags`
+
+* * *
+
+
+# Make changes to the container and Create the new image
+
+Create a folder, for example:
+
+```bash
+docker run -dP systempipe/systempipe_docker
+docker ps ## To check the NAME
+docker exec -it lucid_grothendieck /bin/bash
+root@33c758eb1626:/# R
+```
+
+
+```bash
+setwd("home/rstudio/")
+systemPipeRdata::genWorkenvir("rnaseq")
+```
+
+
+```bash
+exit
+docker commit -m "Added rnaseq template" -a "Dani Cassol" lucid_grothendieck dcassol/systempipeworkshop2021:rnaseq
+docker push systempipe/systempipe_docker:rnaseq
+```
+
+Run the new image:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 systempipe/systempipe_docker:rnaseq
+```
+
+* * *
+
+
+# Commands
+
+## List which docker machines are available locally
+```{bash, eval=FALSE}docker images```
+
+## List running containers
+```{bash, eval=FALSE}docker ps```
+
+## List all containers
+```{bash, eval=FALSE}docker ps -a```
+
+## Resume a stopped container
+```{bash, eval=FALSE}docker start ```
+
+## Shell into a running container
+```{bash, eval=FALSE}docker exec -it /bin/bash```
+
+## Stop OR remove a cointainer
+```{bash, eval=FALSE}docker stop ```
+```{bash, eval=FALSE}docker rm ```
+
+## Remove a image
+```{bash, eval=FALSE}docker rmi dcassol/systempipeworkshop2021:rnaseq```
+
+* * *
+
+
+# Docker and GitHub Actions
+
+1. To create a new token, go to Docker Hub Settings
+
+1.1. Account Settings >> Security >> New Access Token
+1.2. Add Access Token Description >> Create
+1.3. Copy the Access Token >> Copy and Close
+
+2. Go to the Repository at GitHub
+
+2.1. Settings > Secrets > New repository secret
+2.2. Create a new secret with the name `DOCKER_HUB_USERNAME` and your `Docker ID` as value
+2.3. Click at Add secret
+2.4. Create a new secret with the name `DOCKER_HUB_ACCESS_TOKEN` and your `Personal Access Token (PAT)` as value (generated in the previous step)
+
+3. Set up the GitHub Actions workflow
+
+
+```bash
+ steps:
+
+ - name: Checkout Repo
+ uses: actions/checkout@v2
+
+ - name: Login to Docker Hub
+ uses: docker/login-action@v1
+ with:
+ username: ${{ secrets.DOCKER_HUB_USERNAME }}
+ password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+```
+
+* * *
+
+
+
+# Common Problems
+
+
+```bash
+## Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.24/auth: dial unix /var/run/docker.sock: connect: permission denied
+```
+
+Solution:
+
+```bash
+sudo chmod 666 /var/run/docker.sock
+```
+
+* * *
+
+
+# Singularity Container
+
+Please download the Docker image of systemPipe, as follow:
+
+
+```bash
+singularity pull docker://systempipe/systempipe_docker:latest
+```
+
+You can also use the `build` command to download pre-built images from Docker.
+Unlike `pull`, `build` will convert the image to the latest Singularity image format after
+downloading it.
+
+
+```bash
+singularity build systempipe_docker_latest.sif docker://systempipe/systempipe_docker:latest
+```
+
+To run the container:
+
+
+```bash
+singularity shell systempipe_docker_latest.sif
+```
+
+* * *
+
+
+# Resources
+
+- [Docker Run: How to create images from an application](https://www.mirantis.com/blog/how-do-i-create-a-new-docker-image-for-my-application/)
+- [Docker Hub Quickstart](https://docs.docker.com/docker-hub/)
+- [Configure GitHub Actions](https://docs.docker.com/ci-cd/github-actions/)
+- [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#interact-with-images)
diff --git a/content/en/sps/_index.md b/content/en/sps/_index.md
index 5a92b38d1..12144dc38 100644
--- a/content/en/sps/_index.md
+++ b/content/en/sps/_index.md
@@ -82,6 +82,9 @@ For the login required demos, the app account name is **"user"** password **"use
For the admin panel login, account name **"admin"**, password **"admin"**.
+**Please DO NOT delete or change password when you are using the admin features.**
+_shinyapp.io_ will reset the app once a while, but this will affect other people
+who are trying the demo simultaneously.
## Other packages in systemPipeShiny
diff --git a/content/en/sps/adv_features/config.Rmd b/content/en/sps/adv_features/config.Rmd
index da22909e9..d9bb5fe6e 100644
--- a/content/en/sps/adv_features/config.Rmd
+++ b/content/en/sps/adv_features/config.Rmd
@@ -30,7 +30,6 @@ spsInit()
sps_dir <- normalizePath(".")
```
-
```{r echo=FALSE, results='asis'}
options(crayon.enabled = TRUE)
old_hooks <- fansi::set_knit_hooks(knitr::knit_hooks, which = c("output", "message", "error", "warning"))
@@ -131,7 +130,9 @@ options(sps = list(
module_wf = TRUE,
module_rnaseq = TRUE,
module_ggplot = TRUE,
- traceback = FALSE
+ traceback = FALSE,
+ is_demo = FALSE,
+ welcome_guide = TRUE
))
```
@@ -150,17 +151,19 @@ messages on console to tell you specifically what is wrong with your options.
PRE.fansi SPAN {padding-top: .25em; padding-bottom: .25em};
@@ -128,10 +127,10 @@ spsOptDefaults(app_path = sps_dir)
## Default: local
## Other: server
## login_screen:
-## Default: TRUE
-## Other: FALSE
+## Default: FALSE
+## Other: TRUE
## login_theme:
-## Default: vhelix
+## Default: random
## Other: *
## use_crayon:
## Default: TRUE
@@ -140,14 +139,14 @@ spsOptDefaults(app_path = sps_dir)
## Default: FALSE
## Other: TRUE
## admin_page:
-## Default: FALSE
-## Other: TRUE
+## Default: TRUE
+## Other: FALSE
## admin_url:
## Default: admin
## Other: *
## warning_toast:
-## Default: TRUE
-## Other: FALSE
+## Default: FALSE
+## Other: TRUE
## module_wf:
## Default: TRUE
## Other: FALSE
@@ -175,6 +174,12 @@ spsOptDefaults(app_path = sps_dir)
## traceback:
## Default: FALSE
## Other: TRUE
+## is_demo:
+## Default: FALSE
+## Other: TRUE
+## welcome_guide:
+## Default: TRUE
+## Other: FALSE
## * means any value will be accepted
@@ -186,10 +191,48 @@ spsOptions(app_path = sps_dir)
```
## Current project option settings:
-## verbose:
+## title:
+## systemPipeShiny
+## title_logo:
+## img/sps_small.png
+## mode:
+## local
+## login_screen:
## FALSE
+## login_theme:
+## random
## use_crayon:
## TRUE
+## verbose:
+## FALSE
+## admin_page:
+## TRUE
+## admin_url:
+## admin
+## warning_toast:
+## FALSE
+## module_wf:
+## TRUE
+## module_rnaseq:
+## TRUE
+## module_ggplot:
+## TRUE
+## tab_welcome:
+## TRUE
+## tab_vs_main:
+## TRUE
+## tab_canvas:
+## TRUE
+## tab_about:
+## TRUE
+## note_url:
+## https://raw.githubusercontent.com/systemPipeR/systemPipeShiny/master/inst/remote_resource/notifications.yaml
+## traceback:
+## FALSE
+## is_demo:
+## FALSE
+## welcome_guide:
+## TRUE
## ********
## Option legend:
## known options Hidden/custom options* and values+
@@ -220,7 +263,9 @@ options(sps = list(
module_wf = TRUE,
module_rnaseq = TRUE,
module_ggplot = TRUE,
- traceback = FALSE
+ traceback = FALSE,
+ is_demo = FALSE,
+ welcome_guide = TRUE
))
```
@@ -239,17 +284,19 @@ messages on console to tell you specifically what is wrong with your options.## title:
+## Default: systemPipeShiny
+## Other: *
+## title_logo:
+## Default: img/sps_small.png
+## Other: *
+## mode:
+## Default: local
+## Other: server
+## login_screen:
+## Default: FALSE
+## Other: TRUE
+## login_theme:
+## Default: random
+## Other: *
+## use_crayon:
+## Default: TRUE
+## Other: FALSE
+## verbose:
+## Default: FALSE
+## Other: TRUE
+## admin_page:
+## Default: TRUE
+## Other: FALSE
+## admin_url:
+## Default: admin
+## Other: *
+## warning_toast:
+## Default: FALSE
+## Other: TRUE
+## module_wf:
+## Default: TRUE
+## Other: FALSE
+## module_rnaseq:
+## Default: TRUE
+## Other: FALSE
+## module_ggplot:
+## Default: TRUE
+## Other: FALSE
+## tab_welcome:
+## Default: TRUE
+## Other: FALSE
+## tab_vs_main:
+## Default: TRUE
+## Other: FALSE
+## tab_canvas:
+## Default: TRUE
+## Other: FALSE
+## tab_about:
+## Default: TRUE
+## Other: FALSE
+## note_url:
+## Default: https://raw.githubusercontent.com/systemPipeR/systemPipeShiny/master/inst/remote_resource/notifications.yaml
+## Other: *
+## traceback:
+## Default: FALSE
+## Other: TRUE
+## is_demo:
+## Default: FALSE
+## Other: TRUE
+## welcome_guide:
+## Default: TRUE
+## Other: FALSE
+## my_opt1:
+## Default: TRUE
+## Other: FALSE
+## my_opt2:
+## Default: a
+## Other: *
+## * means any value will be accepted
+
+
+You can see the `my_opt1` and `my_opt2` have been added to SPS options.
+
+
+
+
+
+
+
+
+
+
+
diff --git a/content/en/sps/deploy.md b/content/en/sps/deploy.md
index bf92dd040..65f3aecd5 100644
--- a/content/en/sps/deploy.md
+++ b/content/en/sps/deploy.md
@@ -7,11 +7,101 @@ weight: 9
*****
## How to deploy the application
-Among several options of deployment of your `SPS` custom application, here you can find the example of [shinyapps.io](https://www.shinyapps.io/).
-To get started, it is required to create a *shinyapps.io* account. Please follow this [tutorial](https://shiny.rstudio.com/articles/shinyapps.html)
-with all the instructions to create an account.
-`SPS` project provides a ready-to-use file, `deploy.R`, with the required information to configure ShinyApps account and deploy the application.
-
-Once the account is set correctly, you can deploy it as soon as the project is created. It
-is recommended to create -> test/run -> deploy a Shiny app from Rstudio and follow
-[this tutorial](https://shiny.rstudio.com/articles/shinyapps.html).
+The easiest way to deploy SPS is [shinyapps.io{blk}](https://www.shinyapps.io/).
+To get started, it is required to create a *shinyapps.io* account. Please follow this [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html)
+with all the instructions to create an account. There are other ways to deploy, like
+AWS or Google Cloud with a custom Shiny server. There are a lot of tutorials to
+deploy the app other than *shinyapps.io*. We only use *shinyapps.io* as the example
+here to discuss how to deploy.
+
+## Get started
+
+After you have created a `SPS` project, it is in a deploy-ready state, which means
+you can deploy it as soon as you create the project.
+
+We have created some important helper code in `deploy.R` under the project root for you.
+1. Read the [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html)
+2. After you have the accounts and token set up according to the tutorial, open
+ `deploy.R`.
+ - If you have used Bioconductor packages (mostly likely yes, unless you do not use
+ the default modules), run the options line in R console before deploy, which is this
+
+ ```r
+ options(repos = BiocManager::repositories())
+ ```
+
+ - If you want to use develop version of Bioconductor packages (not recommended),
+ uncomment following lines and follow the instructions in the file.
+
+ ```r
+ # repos <- BiocManager::repositories()
+ # devel <- "3.13"
+ # repos[length(repos) + 1] <- paste0("https://bioconductor.org/packages/", devel, "/bioc")
+ # names(repos)[length(repos)] <- "BioC"
+ # options(repos = repos)
+ # getOption("repos")
+ ```
+
+ - If you wish *shinyapps.io* to install [SPS modules](/sps/modules/), copy and
+ **uncomment** following lines for the modules to `global.R` file below the
+ line `# load additional libraries that you want to use below`.
+ ```r
+ ## Workflow module
+ # requireNamespace("DOT"); requireNamespace("networkD3"); requireNamespace("pushbar")
+ # requireNamespace("readr"); requireNamespace("rhandsontable"); requireNamespace("shinyTree")
+ # requireNamespace("systemPipeR"); requireNamespace("systemPipeRdata"); requireNamespace("zip")
+
+ ## RNA-Seq module
+ # requireNamespace("DESeq2"); requireNamespace("Rtsne"); requireNamespace("SummarizedExperiment")
+ # requireNamespace("UpSetR"); requireNamespace("ape"); requireNamespace("ggtree")
+ # requireNamespace("glmpca"); requireNamespace("pheatmap"); requireNamespace("systemPipeR")
+
+ ## Quick ggplot module
+ # requireNamespace("esquisse")
+ ```
+ - The last section in `deploy.R` is some helper code to set up the account and
+ deploy the app programmatically. If you use the
+ [tutorial{blk}](https://shiny.rstudio.com/articles/shinyapps.html),
+ there is no need to do this section.
+ - Save your changes in the `global.R`.
+
+## Deploy in Rstudio
+We recommend you to deploy the app with Rstudio. If you have set up your *shinyapps.io*
+account, we are ready to go.
+
+
+
+
+
+
+
+### A
+1. Open `global.R` in Rstudio, use the "Run App" button to make sure your app
+can be run without problems locally.
+2. Run `options(repos = BiocManager::repositories())` and other Bioconductor
+ set up code as listed above.
+3. Click the button next to "Run App" and choose "Publish Application..."
+
+### B
+4. If you have set up your account correctly, you should see your account to the
+ right panel.
+5. Select all the files of your SPS project.
+6. Change the app "Title" to what you want.
+7. hit "Publish".
+
+## RAM requirement
+
+If you wish to load the workflow and/or RNAseq module(s) on *shinyapps.io*, you need
+at least **2GB** of memory. Unfortunately, these 2 modules depend heavily on Bioconductor
+packages and these packages are not light-weighted. The max RAM for free account
+on *shinyapps.io* is 1GB which means you either need to upgrade your account or
+use other server to deploy your app.
+
+If you decide to not load these modules which will allow you to deploy the app
+with a free account, change the settings to unload these modules in
+[app options](/sps/adv_features/config/#app-options) in `global.R`.
+
+
+
+
+
diff --git a/content/en/sps/img/deploy.png b/content/en/sps/img/deploy.png
new file mode 100644
index 000000000..e1daafda5
Binary files /dev/null and b/content/en/sps/img/deploy.png differ
diff --git a/content/en/sps/modules/workflow.md b/content/en/sps/modules/workflow.md
index b2ecadfb6..2438d9c9c 100644
--- a/content/en/sps/modules/workflow.md
+++ b/content/en/sps/modules/workflow.md
@@ -9,12 +9,12 @@ weight: 1
The workflow management module in `SPS` allows one to modify or create the
configuration files required for running data analysis workflows in
-[systemPipeR](https://systempipe.org/docs/systemPipeR/) (SPR). This includes
+[systemPipeR](https://systempipe.org/sp/spr/) (SPR). This includes
three types of important files: a sample metadata (targets) file, a
workflow file (in R Markdown format) defining the workflow steps, and workflow running
-files in [Common Workflow Language (CWL)](https://www.commonwl.org/) format. In SPS, one can easily create
+files in [Common Workflow Language (CWL){blk}](https://www.commonwl.org/) format. In SPS, one can easily create
these files under the "Workflow Management" module, located in navigation bar
-on the left of the dashboard ([Fig2](/sps/quick_start/#launch-sps)).
+on the [left of the dashboard](/sps/quick_start/#launch-sps).
The current version of `SPS` allows to:
@@ -43,13 +43,13 @@ sequencing workflows.
Clicking the pop-up will jump you to the step 2. The status tracker and banner for
step 1 should all turn green.
-
### 2. Prepare a target file
+
The targets file defines all input file paths and other sample information of
analysis workflows. To better undertand the structure of this file, one can
consult the ["Structure of targets
-file"](https://systempipe.org/docs/systemPipeR/#structure-of-targets-file)
+file"](https://systempipe.org/sp/spr/gettingstarted/#structure-of-targets-file)
section in the SPR vignette. Essentially, this is the tabular file representation
of the `colData` slot in an `SummarizedExperiment` object which stores sample
IDs and other meta information.
@@ -75,7 +75,7 @@ here. Leave it as default for other projects.
### 3. Prepare a workflow file
-In SPR, workflows are defined in Rmarkdown files, you can read details and obtain them [here](https://systempipe.org/pages/pipelines_area/).
+In SPR, workflows are defined in Rmarkdown files, you can read details and obtain them [here](https://systempipe.org/sp/spr/templates/).
Now let us follow the order below to see how SPS helps you to prepare a workflow file for a RNAseq project (Fig.3 B):
@@ -152,3 +152,33 @@ code.
5. Workflow running log.
6. View any plot output. and send a copy of your current plot to SPS Canvas tab or
download it.
+
+
+## App security
+Running the workflow may introduce some security concerns. Read [App Security](/sps/adv_features/app_security/#the-workflow-module)
+for more details.
+
+## `is_demo` option
+The `is_demo` [option](/sps/adv_features/config/#app-options) will impact the workflow
+module.
+- `TRUE`: you are not deploying the app for production purpose. It is just a show case.
+ Under this option, users who are trying to create a workflow will be locked inside
+ a temp directory and every time they start a new session, they will be assigned to
+ a new temp directory. This is useful is many people want to try the app the same
+ time, so they will have private different environment, and the temp directory will
+ be removed afterwards.
+- `FALSE`: you are using the app on your own local computer or use it in a production
+ environment. WF module will have **full access** to the sever storage system and
+ users can choose **any place** they have permission to create the workflow session.
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/content/en/training/Presentations/_index.md b/content/en/training/Presentations/_index.md
index 4a94b7c9e..2705940bd 100644
--- a/content/en/training/Presentations/_index.md
+++ b/content/en/training/Presentations/_index.md
@@ -11,7 +11,7 @@ type: docs
-## [systemPipeRdata{blk}](http://bioconductor.org/packages/devel/bioc/html/systemPipeShiny.html)
+## [systemPipeShiny{blk}](http://bioconductor.org/packages/devel/bioc/html/systemPipeShiny.html)
diff --git a/public/404.html b/public/404.html
index 24c7408ba..234d59108 100644
--- a/public/404.html
+++ b/public/404.html
@@ -45,8 +45,8 @@
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+
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+
+
+
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+
+
+
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+
+
+
+
+
+
+]
+
+
+
+---
+## Structural Features
+
+--
+.left-column[
+#### WF infrastructure
+]
+
+.right-column[
+*systemPipeR* offers many utilities to build, control, and execute
+workflows entirely from R. The environment takes advantage of central community S4 classes
+of the Bioconductor ecosystem. Workflows are managed by generic workflow management
+containers supporting both analysis routines implemented in R code and/or command-line
+software. A layered monitoring infrastructure is provided to design, control and debug each
+step in a workflow. The run environment allows to execute workflows entirely or with a
+intuitive to use step-wise execution syntax using R’s standard subsetting syntax
+(runWF(sys[1:3])) or pipes (%>%).
+]
+
+---
+
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+]
+
+.right-column[
+An important feature of systemPipeR is support for
+running command-line software by adopting the Common Workflow Language (CWL). The
+latter is a widely adopted community standard for describing analysis workflows. This design
+offers several advantages such as:
+
+
+seamless integration of most command-line software
+
+
+support to run systemPipeR workflows from R or many other popular computer languages
+
+
+efficient sharing of workflows across different workflow environments.
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+]
+
+.right-column[
+The processing time of workflows can be greatly reduced by making use
+of parallel evaluations across several CPU cores on single machines, or multiple nodes of
+computer clusters and cloud-based systems. systemPipeR simplifies these parallelization tasks
+without creating any limitations for users who do not have access to high-performance
+computer resources
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+]
+
+.right-column[
+*systemPipeR’s* reporting infrastructure
+includes three types of interconnected reports each serving a different purpose:
+
+
+a scientific report, based on R Markdown, contains all scientifically relevant results
+
+
+a technical report captures all technical information important for each workflow step, including parameter
+settings, software versions, and warning/error messages, etc.
+
+
+a visual report depicts the entire workflow topology including its run status in form of a workflow graph
+
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+#### Shiny Web Interface
+]
+
+.right-column[
+Recently, the systemPipeShiny package has been added that allows
+users to design workflows in an interactive graphical user interface (GUI). In addition to
+designing workflows, this new interface allows users to run and to monitor workflows in an
+intuitive manner without the need of knowing R.
+]
+
+---
+## Structural Features
+
+.left-column[
+#### WF infrastructure
+#### Command-line support
+#### Parallel evaluation
+#### Reports infrastructure
+#### Shiny Web Interface
+#### Workflow Templates
+]
+
+.right-column[
+A rich set of end-to-end workflow templates is provided by this
+project for a wide range omics applications. In addition, users can contribute and share their
+workflows with the community by submitting them to a central GitHub repository
+]
+
+
+---
+## Important Functions
+
+.small[
+| Function Name | Description | Category |
+|-------------------|-----------------------------------------------------------------------------------------------------------------------|-----------------|
+| `genWorkenvir` | Generates workflow templates provided by systemPipeRdata helper package / or from the individuals’ pipelines packages | Accessory |
+| `loadWorkflow` | Constructs `SYSargs2` object from CWL param and targets files | ``SYSargs2`` |
+| `renderWF` | Populate all the command-line in an `SYSargs2` object | ``SYSargs2`` |
+| `subsetWF` | Subsetting `SYSargs2` class slots | ``SYSargs2`` |
+| `runCommandline` | Executes command-line software on samples and parameters specified in `SYSargs2` object | ``SYSargs2`` |
+| `clusterRun` | Runs command-line software in parallel mode on a computer cluster | ``SYSargs2`` |
+| `writeTargetsout` | Write updated targets out to file/Generate targets file with reference | ``SYSargs2`` |
+| `output_update` | Updates the output files paths in the `SYSargs2` object | ``SYSargs2`` |
+| `singleYML` | Create automatically the `param.yml` | ``SYSargs2`` |
+| `createWF` | Create automatically `param.cwl` and the `param.yml` based on the command line | ``SYSargs2`` |
+| `config.param` | Custom configuration of the CWL param files from R | ``SYSargs2`` |
+]
+
+---
+## Important Functions
+
+.small[
+| Function Name | Description | Category |
+|-------------------|-----------------------------------------------------------------------------------------------------------------------|-----------------|
+| `initWF` | Constructs `SYSargsList` workflow control module (S4 object) from script file | ``SYSargsList`` |
+| `configWF` | Control of which step of the workflow will be run and the generation of the new RMarkdown | ``SYSargsList`` |
+| `runWF` | Runs all the R chunk define in the RMarkdown file or a subset, e.g. `runWF[1:3]` | ``SYSargsList`` |
+| `renderReport` | Render Scientific Report based on RMarkdown | ``SYSargsList`` |
+| `subsetRmd` | Write updated subset Rmarkdown of R chunk with text associate in the step selected | ``SYSargsList`` |
+| `plotWF` | Plot visual workflow designs and topologies with different graphical layouts | ``SYSargsList`` |
+| `statusWF` | Return the overview of the workflow steps computational status | ``SYSargsList`` |
+| `evalCode` | Turn eval option `TRUE` or `FALSE` on RMarkdown file | Accessory |
+| `tryCL` | Checks if third-party software or utility is installed and set in the PATH | Accessory |
+]
+
+
+
+
+
+
+---
+class: inverse, center, middle
+
+# Design
+
+---
+### Workflow Management Solutions
+
+
+*systemPipeR* central concept for designing workflows is **workflow
+management containers** (S4 class)
+
+
+*SYSargs2* controls workflow steps with input/output file operations
+
+
+*SYSargs2* requires a targets and a set of workflow definition files (here param.cwl and param.yml)
+
+
+
+
+
+*SYSargsList* objects organize one or many *SYSargs2*
+containers in a single compound object capturing all information required to run, control and
+monitor complex workflows from start to finish
+
+.center[
+
+]
+
+---
+## 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 | |  |
+| [systemPipeRIBOseq](https://systempiper.github.io/systemPipeRIBOseq/articles/systemPipeRIBOseq.html) | RIBO-Seq Workflow Template | v1.0 | |  |
+| [systemPipeRNAseq](https://systempiper.github.io/systemPipeRNAseq/articles/systemPipeRNAseq.html) | RNA-Seq Workflow Template | v1.0 | |  |
+| [systemPipeVARseq](https://systempiper.github.io/systemPipeVARseq/articles/systemPipeVARseq.html) | VAR-Seq Workflow Template | v1.0 | |  |
+| [systemPipeMethylseq](https://github.com/systemPipeR/systemPipeMethylseq) | Methyl-Seq Workflow Template | devel | |  |
+| [systemPipeDeNovo](https://github.com/systemPipeR/systemPipeDeNovo) | De novo transcriptome assembly Workflow Template | devel | |  |
+| [systemPipeCLIPseq](https://github.com/systemPipeR/systemPipeCLIPseq) | CLIP-Seq Workflow Template | devel | |  |
+| [systemPipeMetaTrans](https://github.com/systemPipeR/systemPipeMetaTrans) | Metatranscriptomic Sequencing Workflow Template | devel | |  |
+]
+
+---
+class: inverse, center, middle
+
+# CWL
+
+---
+## CWL
+
+ **TODO:**
+Add section with CWL details
+
+.center[
+
+]
+
+---
+## CWL and SPR
+
+ **TODO:**
+How to use CWL definition with *systemPipeR*
+
+- *SYSargs2* instances are constructed from a *`targets`* file and two *`param`* file
+ - *`hisat2-mapping-se.cwl`* file contains the settings for running command-line software
+ - *`hisat2-mapping-se.yml`* file define all the variables to be input in the specific command-line step
+
+
+```r
+targets <- system.file("extdata", "targets.txt", package="systemPipeR")
+dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
+align <- loadWF(targets=targets, wf_file="hisat2-mapping-se.cwl",
+ input_file="hisat2-mapping-se.yml", dir_path=dir_path)
+align <- renderWF(align, inputvars=c(FileName="_FASTQ_PATH_", SampleName="_SampleName_"))
+
+## Instance of 'SYSargs2':
+## Slot names/accessors:
+## targets: 18 (M1A...V12B), targetsheader: 4 (lines)
+## modules: 2
+## wf: 0, clt: 1, yamlinput: 7 (components)
+## input: 18, output: 18
+## cmdlist: 18
+## WF Steps:
+## 1. hisat2-mapping-se.cwl (rendered: TRUE)
+```
+
+---
+## CWL and SPR
+
+## *`SYSargs2`* instance
+
+- Slots and accessor functions have the same names
+
+```r
+names(align)
+# [1] "targets" "targetsheader" "modules" "wf" "clt"
+# [6] "yamlinput" "cmdlist" "input" "output" "cwlfiles"
+# [11] "inputvars"
+```
+
+- *`cmdlist`* return command-line arguments for the specific software, here *`HISAT2`* for the first sample
+
+```r
+cmdlist(align)[1]
+# $M1A
+# $M1A$`hisat2-mapping-se.cwl`
+# [1] "hisat2 -S results/M1A.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446027_1.fastq.gz --threads 4"
+```
+
+- The output components of *`SYSargs2`* define all the expected output files for each step in the workflow; some of which are the input for the next workflow step
+
+
+```r
+output(align)[1]
+# $M1A
+# $M1A$`hisat2-mapping-se.cwl`
+# [1] "results/M1A.sam"
+```
+
+---
+class: inverse, center, middle
+
+# Metadata
+
+---
+### *Targets* file organizes samples
+
+- Structure of *`targets`* file for single-end (SE) library
+
+```r
+targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:3,1:4]
+```
+
+```
+## FileName SampleName Factor SampleLong
+## 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A
+## 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B
+## 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A
+```
+
+- Structure of *`targets`* file for paired-end (PE) library
+
+```r
+targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:3,1:5]
+```
+
+```
+## FileName1 FileName2 SampleName Factor
+## 1 ./data/SRR446027_1.fastq.gz ./data/SRR446027_2.fastq.gz M1A M1
+## 2 ./data/SRR446028_1.fastq.gz ./data/SRR446028_2.fastq.gz M1B M1
+## 3 ./data/SRR446029_1.fastq.gz ./data/SRR446029_2.fastq.gz A1A A1
+## SampleLong
+## 1 Mock.1h.A
+## 2 Mock.1h.B
+## 3 Avr.1h.A
+```
+
+---
+### Integration with *SummarizedExperiment*
+
+- Integrates *targets* files and count table from *systemPipeR* to a *SummarizedExperiment* object
+
+
+```r
+## Create an object with targets file and comparison and count table
+sprSE <- SPRdata(targetspath = targetspath, cmp=TRUE)
+metadata(sprSE)
+# $version
+# [1] ‘1.23.9’
+#
+# $comparison
+# $comparison$CMPset1
+# [,1] [,2]
+# [1,] "M1" "A1"
+# [2,] "M1" "V1"
+# [3,] "A1" "V1"
+# [4,] "M6" "A6"
+
+colData(sprSE)
+# DataFrame with 18 rows and 6 columns
+# FileName SampleName Factor SampleLong
+#
+]
+
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+]
+
+.right-column[
+
+```r
+library(systemPipeR)
+targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
+read.delim(targetspath, comment.char = "#")[1:4,1:4]
+```
+
+```
+## FileName SampleName Factor SampleLong
+## 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A
+## 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B
+## 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A
+## 4 ./data/SRR446030_1.fastq.gz A1B A1 Avr.1h.B
+```
+
+```r
+script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- initWF(script = script, targets = targetspath, overwrite = TRUE)
+# Project started with success: ./SYSproject and SYSconfig.yml were created.
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- configWF(sysargslist, input_steps = "1:3")
+sysargslist
+# Instance of 'SYSargsList':
+# WF Steps:
+# 1. Rmarkdown/HTML setting
+# 2. Introduction
+# 3. Samples and environment settings
+# 3.1. Environment settings and input data
+# 3.2. Required packages and resources
+# 3.3. Experiment definition provided by `targets` file
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+### `runWF`
+]
+
+.right-column[
+
+```r
+sysargslist <- runWF(sysargslist, steps = "1:2")
+# Step: 1: Introduction --> DONE
+# Step: 2: Samples and environment settings --> DONE
+# Step: 2.1: Environment settings and input data --> DONE
+# Step: 2.2: Required packages and resources --> DONE
+# Step: 2.3: Experiment definition provided by `targets` file --> DONE
+```
+
+
+```r
+sysargslist <- runWF(sysargslist, steps = "ALL")
+```
+]
+
+---
+## Run a Workflow
+
+.left-column[
+### Setup
+### `initWF`
+### `configWF`
+### `runWF`
+### `renderReport`
+]
+
+.right-column[
+
+```r
+sysargslist <- renderReport(sysargslist = sysargslist)
+```
+]
+
+---
+## How to Use Pipes `%>%`
+
+Consider the following example, in which the steps are the initialization, configuration and running the entire workflow.
+
+
+```r
+library(systemPipeR)
+sysargslist <- initWF(script ="systemPipeRNAseq.Rmd", overwrite = TRUE) %>%
+ configWF(input_steps = "1:6") %>%
+ runWF(steps = "1:2")
+```
+
+---
+class: inverse, center, middle
+
+# Project Updates
+
+---
+### *targets* x *SummarizedExperiment*
+
+Extension "SummarizedExperiment" methods:
+
+
+```r
+sprSE <- addAssay(sprSE, assay(countMatrix), xName="countMatrix")
+sprSE <- addMetadata(sprSE, list(targets), xName="metadata")
+```
+
+
+New Function:
+
+
+```r
+## Create empty SummarizedExperiment
+sprSE <- SPRdata()
+
+## Create an object with targets file and comparison and count table
+sprSE <- SPRdata(counts = countMatrix, cmp=TRUE, targetspath = targetspath)
+metadata(sprSE)
+colData(sprSE)
+assays(sprSE)
+```
+
+---
+## SPR Paper
+
+
+[Link to draft](https://www.overleaf.com/project/5e94948a23918a000116311c)
+
+
+Added the main points to discuss in the draft
+
+
+Writing: Results and introduction
+
+
+Improve Graphical Abstract
+
+
+Show case?
+
+---
+## *SYSargsList*
+
+
+Explain how *SYSargsList* is implemented - Vignette
+
+.small[
+| Function Name | Description |
+|----------------|-------------------------------------------------------------------------------------------|
+| `initWF` | Constructs `SYSargsList` workflow control module (S4 object) from script file |
+| `configWF` | Control of which step of the workflow will be run and the generation of the new RMarkdown |
+| `runWF` | Runs all the R chunk define in the RMarkdown file or a subset, e.g. `runWF[1:3]` |
+| `renderReport` | Render Scientific Report based on RMarkdown |
+| `renderLog` | Render logs Report based on RMarkdown |
+| `updateWF` | Recover the `SYSargsList` workflow previous ran and restarts the WF |
+| `plotWF` | Plot visual workflow designs and topologies with different graphical layouts |
+| `statusWF` | Return the overview of the workflow steps computational status |
+| `evalCode` | Turn eval option `TRUE` or `FALSE` on RMarkdown file |
+| `tryCL` | Checks if third-party software or utility is installed and set in the PATH |
+]
+
+
+Improve `statusWF()`
+
+---
+## Visualization in *systemPipeR*
+
+
+Add to vignette (SPR or SPS)
+ - `exploreDDS`, `exploreDDSplot`, `GLMplot`, `MAplot`, `MDSplot`, `PCAplot`, `hclustplot`, `heatMaplot`, `tSNEplot`, `volcanoplot`
+
+
+Enrichment analysis and visualization tool for SPR
+- Integration with `FGSEA`
+
+
+---
+## WebSite
+
+
+Updated the vignette
+
+
+Added *systemPipeRdata* vignette and presentation: [link](https://systempipe.org/docs/systemPipeRdata/)
+
+
+Redirect http://girke.bioinformatics.ucr.edu/systemPipeR/ to new page
+
+
+Add content to FAQ section
+
+
+Add tutorials videos
+
+---
+class: middle
+
+# Thanks!
+
+
+Browse source code at
+
+
+Ask a question about systemPipeR at Bioconductor Support Page
+
+
+
+*systemPipeRdata* at [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
+
+
+[https://systempipe.org/](https://systempipe.org/)
+
diff --git a/content/en/presentations/SPR/libs/tile-view/tile-view.js b/content/en/presentations/SPR/libs/tile-view/tile-view.js
index 7aac71611..bb31dc2fa 100644
--- a/content/en/presentations/SPR/libs/tile-view/tile-view.js
+++ b/content/en/presentations/SPR/libs/tile-view/tile-view.js
@@ -44,6 +44,10 @@
el.style.display = el.style.display === 'none' ? '' : 'none'
}
+ function slideshowResize () {
+ window.dispatchEvent(new Event('resize'))
+ }
+
const toggleTileView = function () {
toggleElement(tileView)
toggleElement(remarkSlideShow)
@@ -52,11 +56,8 @@
// tileView is now hidden, go to current slide
slideshow.gotoSlide(tileVars.currentSlideIdx + 1)
- // remove scroll/mousewheel event blocking
- tileView.removeEventListener('mousewheel', blockEvent)
- tileView.removeEventListener('DOMMouseScroll', blockEvent)
- console.log('removing blockScaling')
- document.removeEventListener('keydown', blockScaling)
+ slideshow.resume()
+ slideshowResize()
} else {
// store current slide index prior to launching tile-view
tileVars.currentSlideIdx = slideshow.getCurrentSlideIndex()
@@ -78,11 +79,7 @@
block: 'center'
})
- // block remarkjs from handling scroll events
- tileView.addEventListener('mousewheel', blockEvent)
- tileView.addEventListener('DOMMouseScroll', blockEvent)
- console.log('adding blockScaling')
- document.addEventListener('keydown', blockScaling)
+ slideshow.pause()
}
}
@@ -150,15 +147,6 @@
}
const tileVars = {}
- const blockEvent = ev => ev.stopPropagation()
- const blockScaling = function (ev) {
- if (ev.controlKey || ev.metaKey) {
- if (ev.key === '=' || ev.key === '-') {
- ev.preventDefault()
- console.log('window scaling is not allowed inside the tile overview')
- }
- }
- }
document.addEventListener('keydown', ev => {
if (ev.keyCode === launchKey) {
diff --git a/content/en/presentations/SPS/SPS_intro.knit.md b/content/en/presentations/SPS/SPS_intro.md
similarity index 100%
rename from content/en/presentations/SPS/SPS_intro.knit.md
rename to content/en/presentations/SPS/SPS_intro.md
diff --git a/content/en/sp/SPR/SP_docker.md b/content/en/sp/SPR/SP_docker.md
new file mode 100644
index 000000000..7513c10cb
--- /dev/null
+++ b/content/en/sp/SPR/SP_docker.md
@@ -0,0 +1,425 @@
+---
+title: "SPR Docker container"
+author: "Author: Daniela Cassol (danielac@ucr.edu)"
+date: "Last update: 25 April, 2021"
+output:
+ BiocStyle::html_document:
+ toc_float: true
+ code_folding: show
+ BiocStyle::pdf_document: default
+package: systemPipeR
+fontsize: 14pt
+type: docs
+weight: 8
+---
+
+> Guidelines from [bioconductor_docker](https://github.com/Bioconductor/bioconductor_docker).
+
+# Running the `systemPipeR` with Docker
+
+## Get a copy of the public docker image
+
+
+```bash
+docker pull systempipe/systempipe_docker:latest
+```
+
+## To run RStudio Server:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 \
+ systempipe/systempipe_docker:latest
+```
+
+You can then open a web browser pointing to your docker host on
+port 8787. If you're on Linux and using default settings, the docker
+host is `127.0.0.1` (or `localhost`, so the full URL to RStudio would
+be `http://localhost:8787)`. If you are on Mac or Windows and running
+`Docker Toolbox`, you can determine the docker host with the
+`docker-machine ip default` command.
+
+In the above command, `-e PASSWORD=` is setting the RStudio password
+and is required by the RStudio Docker image. It can be whatever you
+like except it cannot be `rstudio`. Log in to RStudio with the
+username `rstudio` and whatever password was specified, in this
+example `systemPipe`.
+
+## To run R from the command line:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest R
+```
+
+## To open a Bash shell on the container:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest bash
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+* * *
+
+
+# Install
+
+**Prerequisites**:
+[Linux](https://docs.docker.com/installation/)
+[Mac](http://docs.docker.com/installation/mac/)
+[Windows](http://docs.docker.com/installation/windows/)
+
+Instructions [here](https://docs.docker.com/engine/install/ubuntu/) on how to install Docker Engine on Ubuntu.
+
+
+```bash
+sudo apt-get update
+sudo apt-get install \
+ apt-transport-https \
+ ca-certificates \
+ curl \
+ gnupg
+curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+echo \
+ "deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
+ $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo apt-get update
+sudo apt-get install docker-ce docker-ce-cli containerd.io
+
+## Verify that Docker Engine is installed correctly by running the hello-world image.
+sudo docker run hello-world
+```
+
+## Uninstall
+
+
+```bash
+sudo apt-get remove docker docker-engine docker.io containerd runc
+```
+* * *
+
+
+# Docker Hub Account
+
+To be able to share a custom image, please go to https://hub.docker.com and
+create a free account.
+
+* * *
+
+
+## Log in to the Docker Hub locally
+
+Login with your Docker ID to push and pull images from Docker Hub. If you don't
+have a Docker ID, head over to https://hub.docker.com to create one.
+
+
+```bash
+docker login
+# Username: XXXX
+# Password: xxx
+# Login Succeeded
+```
+
+* * *
+
+
+# Run Docker
+
+
+```bash
+docker run-dP systempipe/systempipe_docker:latest
+```
+
+Make sure the container is running:
+
+```bash
+docker ps
+# CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS # NAMES
+#5d007f66a7b3 systempipe/systempipe_docker:latest "/init" 5 minutes ago Up 5 minutes 0.0.0.0:49153->8787/tcp determined_easle
+```
+
+## Login to the container
+
+Please check the `NAMES` in this example, `determined_easle,` to login into the container.
+
+
+```bash
+docker exec -it determined_easle /bin/bash
+```
+
+## Other alternatives to run the container
+
+### To run RStudio Server:
+
+
+```bash
+docker run -e PASSWORD=systemPipe -p 8787:8787 \
+ systempipe/systempipe_docker:latest
+```
+
+### To run R from the command line:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest R
+```
+
+### To open a Bash shell on the container:
+
+
+```bash
+docker run -it --user rstudio systempipe/systempipe_docker:latest bash
+```
+
+### Check R Version into the container
+
+
+```bash
+R --version
+```
+## Stop Docker
+
+
+```bash
+docker stop determined_easle
+```
+
+* * *
+
+
+# Create your first repository [Link](https://docs.docker.com/docker-hub/)
+
+## Create a repository:
+
+- Sign in to Docker Hub.
+- Click Create a Repository on the Docker Hub welcome page:
+- Name it ## Current project option settings:
-## verbose:
+## title:
+## systemPipeShiny
+## title_logo:
+## img/sps_small.png
+## mode:
+## local
+## login_screen:
## FALSE
+## login_theme:
+## random
## use_crayon:
## TRUE
+## verbose:
+## FALSE
+## admin_page:
+## TRUE
+## admin_url:
+## admin
+## warning_toast:
+## FALSE
+## module_wf:
+## TRUE
+## module_rnaseq:
+## TRUE
+## module_ggplot:
+## TRUE
+## tab_welcome:
+## TRUE
+## tab_vs_main:
+## TRUE
+## tab_canvas:
+## TRUE
+## tab_about:
+## TRUE
+## note_url:
+## https://raw.githubusercontent.com/systemPipeR/systemPipeShiny/master/inst/remote_resource/notifications.yaml
+## traceback:
+## FALSE
+## is_demo:
+## FALSE
+## welcome_guide:
+## TRUE
## ********
## Option legend:
## known options Hidden/custom options* and values+
@@ -220,7 +263,9 @@ options(sps = list(
module_wf = TRUE,
module_rnaseq = TRUE,
module_ggplot = TRUE,
- traceback = FALSE
+ traceback = FALSE,
+ is_demo = FALSE,
+ welcome_guide = TRUE
))
```
@@ -239,17 +284,19 @@ messages on console to tell you specifically what is wrong with your options.## title:
+## Default: systemPipeShiny
+## Other: *
+## title_logo:
+## Default: img/sps_small.png
+## Other: *
+## mode:
+## Default: local
+## Other: server
+## login_screen:
+## Default: FALSE
+## Other: TRUE
+## login_theme:
+## Default: random
+## Other: *
+## use_crayon:
+## Default: TRUE
+## Other: FALSE
+## verbose:
+## Default: FALSE
+## Other: TRUE
+## admin_page:
+## Default: TRUE
+## Other: FALSE
+## admin_url:
+## Default: admin
+## Other: *
+## warning_toast:
+## Default: FALSE
+## Other: TRUE
+## module_wf:
+## Default: TRUE
+## Other: FALSE
+## module_rnaseq:
+## Default: TRUE
+## Other: FALSE
+## module_ggplot:
+## Default: TRUE
+## Other: FALSE
+## tab_welcome:
+## Default: TRUE
+## Other: FALSE
+## tab_vs_main:
+## Default: TRUE
+## Other: FALSE
+## tab_canvas:
+## Default: TRUE
+## Other: FALSE
+## tab_about:
+## Default: TRUE
+## Other: FALSE
+## note_url:
+## Default: https://raw.githubusercontent.com/systemPipeR/systemPipeShiny/master/inst/remote_resource/notifications.yaml
+## Other: *
+## traceback:
+## Default: FALSE
+## Other: TRUE
+## is_demo:
+## Default: FALSE
+## Other: TRUE
+## welcome_guide:
+## Default: TRUE
+## Other: FALSE
+## my_opt1:
+## Default: TRUE
+## Other: FALSE
+## my_opt2:
+## Default: a
+## Other: *
+## * means any value will be accepted
+
+
+
+
+
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+
+
+
+
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+