no_render

Author: Thomas Girke

.Rprofile

@@ -1,7 +1,8 @@
 cat("Set up hugo variables\n")
 Sys.setenv(HUGO_ENV="production")
 options(blogdown.method = 'markdown')
-options(blogdown.hugo.version = "0.87.0")
+# options(blogdown.hugo.version = "0.87.0")
+options(blogdown.hugo.version = "0.123.7")
 #options(blogdown.method = "markdown")
 if(interactive()){
   cat("Launching website with Hugo\n")

config.toml

@@ -20,7 +20,8 @@ defaultContentLanguageInSubdir = false
 # Useful when translating.
 enableMissingTranslationPlaceholders = true
 
-disableKinds = ["taxonomy", "taxonomyTerm"]
+## old: disableKinds = ["taxonomy", "taxonomyTerm"]
+disableKinds = ["taxonomy", "RSS"]
 
 # Highlighting config
 pygmentsCodeFences = false
@@ -58,11 +59,14 @@ id = "UA-158796879-1"
 
 [languages]
 [languages.en]
-title = "sysPipe"
-description = "systemPipe Workflow Environment"
-languageName ="English"
-time_format_default = "2006-01-02"
-time_format_blog = "2006-01-02"
+languageName = "English"
+# Keep standard Hugo settings (like title, weight, languageName) here.
+
+  [languages.en.params] 
+  description = "systemPipe Workflow Environment"
+  time_format_default = "2006-01-02"
+  time_format_blog = "2006-01-02"
+
 ## Weight used for sorting.
 ## uncomment below for more than one language support
 #weight = 1

content/en/about/_index.md

@@ -2,44 +2,8 @@
 title: "About systemPipe Project"
 linkTitle: "About"
 type: docs
-exclude_search: true
-date: "Last update: 29 April, 2022" 
-package: systemPipeR
 ---
 
-{{% pageinfo %}}
-[systemPipeR{blk}](https://www.bioconductor.org/packages/release/bioc/vignettes/systemPipeR/inst/doc/systemPipeR.html) and [systemPipeShiny{blk}](https://systempipe.org/sps/) full documentation!
-{{% /pageinfo %}}
-
-systemPipe (SP) is a generic toolkit for designing and running reproducible data 
-analysis workflows. The environment consists of three major modules implemented
-as R/Bioconductor packages. 
-
-<img src="systemPipe_logo.png" width="50%" style="display: block; margin: auto;" />
-
-- _systemPipeR_ (SPR) provides core functionalities for defining workflows, 
-interacting with command-line software, and executing both R and/or command-line 
-software, as well as generating publication-quality analysis reports. 
-- _systemPipeData_ (SPRdata) offers a collection of pre-configured workflow templates.
-- _systemPipeShiny_ (SPS) integrates a graphical user interface for managing 
-workflows and visualizing results interactively. 
-
- ### Availability
-
-All the packages are freely available for all common operating systems from
-[Bioconductor{blk}](http://bioconductor.org/packages/systemPipeR). 
-
-- _systemPipeR_: [Bioconductor{blk}](http://bioconductor.org/packages/systemPipeR) and [Github{blk}](https://github.com/tgirke/systemPipeR)
-
-- _systemPipeShiny_: [Bioconductor{blk}](http://bioconductor.org/packages/release/bioc/html/systemPipeShiny.html) and [Github{blk}](https://github.com/systemPipeR/systemPipeShiny)
-
-- _systemPipeWorkflow_: [Github{blk}](https://github.com/systemPipeR)
-
-## Acknowledgement
-
-This project is funded by NSF award [ABI-1661152{blk}](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661152).
-
-
 
 
 

content/en/about/bak_index.md

@@ -0,0 +1,46 @@
+---
+title: "About systemPipe Project"
+linkTitle: "About"
+type: docs
+exclude_search: true
+date: "Last update: 29 April, 2022" 
+package: systemPipeR
+---
+
+{{% pageinfo %}}
+[systemPipeR{blk}](https://www.bioconductor.org/packages/release/bioc/vignettes/systemPipeR/inst/doc/systemPipeR.html) and [systemPipeShiny{blk}](https://systempipe.org/sps/) full documentation!
+{{% /pageinfo %}}
+
+systemPipe (SP) is a generic toolkit for designing and running reproducible data 
+analysis workflows. The environment consists of three major modules implemented
+as R/Bioconductor packages. 
+
+<img src="systemPipe_logo.png" width="50%" style="display: block; margin: auto;" />
+
+- _systemPipeR_ (SPR) provides core functionalities for defining workflows, 
+interacting with command-line software, and executing both R and/or command-line 
+software, as well as generating publication-quality analysis reports. 
+- _systemPipeData_ (SPRdata) offers a collection of pre-configured workflow templates.
+- _systemPipeShiny_ (SPS) integrates a graphical user interface for managing 
+workflows and visualizing results interactively. 
+
+ ### Availability
+
+All the packages are freely available for all common operating systems from
+[Bioconductor{blk}](http://bioconductor.org/packages/systemPipeR). 
+
+- _systemPipeR_: [Bioconductor{blk}](http://bioconductor.org/packages/systemPipeR) and [Github{blk}](https://github.com/tgirke/systemPipeR)
+
+- _systemPipeShiny_: [Bioconductor{blk}](http://bioconductor.org/packages/release/bioc/html/systemPipeShiny.html) and [Github{blk}](https://github.com/systemPipeR/systemPipeShiny)
+
+- _systemPipeWorkflow_: [Github{blk}](https://github.com/systemPipeR)
+
+## Acknowledgement
+
+This project is funded by NSF award [ABI-1661152{blk}](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661152).
+
+
+
+
+
+

content/en/sp/spr/steps.md

@@ -529,7 +529,7 @@ identifying differentially expressed genes (DEGs) in batch mode with
 *`edgeR`*’s GML method (Robinson, McCarthy, and Smyth 2010) for any number of
 pairwise sample comparisons specified under the *`cmp`* argument. Users
 are strongly encouraged to consult the
-[*`edgeR`*](\href%7Bhttp://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) vignette
+[*`edgeR`*](http://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) vignette
 for more detailed information on this topic and how to properly run *`edgeR`*
 on data sets with more complex experimental designs.
 

content/en/sp/spr/steps_oldVersion.md

@@ -864,8 +864,8 @@ identifying differentially expressed genes (DEGs) in batch mode with
 *`edgeR`*’s GML method (Robinson, McCarthy, and Smyth 2010) for any number of
 pairwise sample comparisons specified under the *`cmp`* argument. Users
 are strongly encouraged to consult the
-[*`edgeR`*](\href%7Bhttp://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) vignette
-for more detailed information on this topic and how to properly run *`edgeR`*
+[edgeR](http://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf)
+vignette for more detailed information on this topic and how to properly run *`edgeR`*
 on data sets with more complex experimental designs.
 
 ``` r

mybuild.sh

@@ -3,6 +3,14 @@
 ###################################################################
 ## Thomas added on 01-Dec-2025
 
+## New git clone instance
+git clone git@github.com:systemPipeR/systemPipeR.github.io.git
+git submodule update --init --recursive
+## if there is an error blogdown loading site pay attetion to version .Rprofile
+# options(blogdown.hugo.version = "0.87.0")
+options(blogdown.hugo.version = "0.123.7")
+
+
 ## One necessary fix (one time setup change) was to ignore jekyll in build, which gave errors
 ## under github actions. Adding a .nojekyll file fixed this.
 git checkout main # just in case
@@ -14,10 +22,28 @@ git push
 ## Deploy site from local
 git checkout main # just in case
 hugo --verbose --cleanDestinationDir # build site. This creates rendered html files under `public/` 
+#-> in new version use instead of --verbose: logLevel info
 cp .nojekyll public
 git add . # needs to be done to account for changes in `public/`
 git commit -am "no_render" # tell github action not to render. 
 git push origin main
 git push origin `git subtree split --prefix public`:gh-pages --force # use only to resolve possible error in push
 # git subtree push --prefix public origin gh-pages # alternative not used
 
+
+# 1. Build the site
+hugo --cleanDestinationDir 
+
+# 2. Safety copy of .nojekyll (just in case)
+cp .nojekyll public/
+
+# 3. Stage and Commit
+git add . 
+git commit -m "Fix config warnings and update site"
+
+# 4. Push Source to Main
+git push origin main
+
+# 5. Force Push to gh-pages (Your standard deployment command)
+git push origin `git subtree split --prefix public`:gh-pages --force
+