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systemPipeR · Aug 7, 2021 · 171d9df · 171d9df
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diff --git a/.Rprofile b/.Rprofile
@@ -7,3 +7,5 @@ if(interactive()){
   blogdown::serve_site()
 }
 cat("Done\n")
+Sys.setenv(`_R_CHECK_LENGTH_1_LOGIC2_`='false')
+Sys.setenv(`_R_CHECK_LENGTH_1_CONDITION_`='false')
diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/cleaning_099c5009c8c8298a23befa3ba15f24d7.RData
diff --git a/...ines_e3ec03c8a070638cf7d0da0fda75ab0e.rdb → ...ning_099c5009c8c8298a23befa3ba15f24d7.rdb b/...ines_e3ec03c8a070638cf7d0da0fda75ab0e.rdb → ...ning_099c5009c8c8298a23befa3ba15f24d7.rdb
diff --git a/...ines_e3ec03c8a070638cf7d0da0fda75ab0e.rdx → ...ning_099c5009c8c8298a23befa3ba15f24d7.rdx b/...ines_e3ec03c8a070638cf7d0da0fda75ab0e.rdx → ...ning_099c5009c8c8298a23befa3ba15f24d7.rdx
diff --git a/.../en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.RData b/.../en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.RData
diff --git a/...wn/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.rdb b/...wn/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.rdb
diff --git a/...wn/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.rdx b/...wn/en/sp/spr/gettingstarted_cache/html/comment_lines_a751a89d87bb00e5f1af74a63fb49a1c.rdx
diff --git a/.../en/sp/spr/gettingstarted_cache/html/comment_lines_e3ec03c8a070638cf7d0da0fda75ab0e.RData b/.../en/sp/spr/gettingstarted_cache/html/comment_lines_e3ec03c8a070638cf7d0da0fda75ab0e.RData
diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/dir_b02548596581cc51ed0b95fa5320988c.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/dir_b02548596581cc51ed0b95fa5320988c.RData
diff --git a/...comp_56fb67d22a9259587b2fc50299954f27.rdb → .../dir_b02548596581cc51ed0b95fa5320988c.rdb b/...comp_56fb67d22a9259587b2fc50299954f27.rdb → .../dir_b02548596581cc51ed0b95fa5320988c.rdb
diff --git a/...comp_56fb67d22a9259587b2fc50299954f27.rdx → .../dir_b02548596581cc51ed0b95fa5320988c.rdx b/...comp_56fb67d22a9259587b2fc50299954f27.rdx → .../dir_b02548596581cc51ed0b95fa5320988c.rdx
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diff --git a/...wn/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdb b/...wn/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdb
diff --git a/...wn/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdx b/...wn/en/sp/spr/gettingstarted_cache/html/documentation_3369537b5da7730cafdc54b7e06bce1a.rdx
diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.RData b/blogdown/en/sp/spr/gettingstarted_cache/html/install_0ebfe8510aceb616bf6e78aee75d88e2.RData
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diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdb
diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/setup_364d4b0afd20170202ebe6c445f9700f.rdx
diff --git a/...own/en/sp/spr/gettingstarted_cache/html/targetsFig_a7fc115b2c51f2ae9852c233e1272078.RData b/...own/en/sp/spr/gettingstarted_cache/html/targetsFig_a7fc115b2c51f2ae9852c233e1272078.RData
diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_a7fc115b2c51f2ae9852c233e1272078.rdb b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_a7fc115b2c51f2ae9852c233e1272078.rdb
diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_a7fc115b2c51f2ae9852c233e1272078.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsFig_a7fc115b2c51f2ae9852c233e1272078.rdx
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diff --git a/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_c4e42d1de7980e8dff2ec741a14284a9.rdx b/blogdown/en/sp/spr/gettingstarted_cache/html/targetsPE_c4e42d1de7980e8dff2ec741a14284a9.rdx
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diff --git a/...wn/en/sp/spr/gettingstarted_cache/html/targetscomp_56fb67d22a9259587b2fc50299954f27.RData b/...wn/en/sp/spr/gettingstarted_cache/html/targetscomp_56fb67d22a9259587b2fc50299954f27.RData
diff --git a/...wn/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.RData b/...wn/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.RData
diff --git a/...down/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdb b/...down/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdb
diff --git a/...down/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdx b/...down/en/sp/spr/gettingstarted_cache/html/targetscomp_a16aec4247ee217dbaf82f15ba34e9d0.rdx
diff --git a/blogdown/en/sp/spr/introduction_cache/html/__packages b/blogdown/en/sp/spr/introduction_cache/html/__packages
@@ -0,0 +1,22 @@
+base
+BiocStyle
+BiocGenerics
+S4Vectors
+IRanges
+GenomeInfoDb
+GenomicRanges
+XVector
+Biostrings
+Rsamtools
+BiocParallel
+matrixStats
+MatrixGenerics
+Biobase
+SummarizedExperiment
+GenomicAlignments
+ShortRead
+systemPipeR
+ggplot2
+ape
+batchtools
+magrittr
diff --git a/blogdown/en/sp/spr/introduction_cache/html/setup_7283af093f9a8d7a7cd1e55b1e48b046.RData b/blogdown/en/sp/spr/introduction_cache/html/setup_7283af093f9a8d7a7cd1e55b1e48b046.RData
diff --git a/blogdown/en/sp/spr/introduction_cache/html/setup_7283af093f9a8d7a7cd1e55b1e48b046.rdb b/blogdown/en/sp/spr/introduction_cache/html/setup_7283af093f9a8d7a7cd1e55b1e48b046.rdb
diff --git a/blogdown/en/sp/spr/introduction_cache/html/setup_7283af093f9a8d7a7cd1e55b1e48b046.rdx b/blogdown/en/sp/spr/introduction_cache/html/setup_7283af093f9a8d7a7cd1e55b1e48b046.rdx
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diff --git a/blogdown/en/sp/spr/spr_run_cache/html/SPR_resume_1e5a79a7e0b1d911251d81ee872212fd.RData b/blogdown/en/sp/spr/spr_run_cache/html/SPR_resume_1e5a79a7e0b1d911251d81ee872212fd.RData
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diff --git a/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_env_11ff08ebee34de16f0bd567d83920f18.rdx b/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_env_11ff08ebee34de16f0bd567d83920f18.rdx
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_logs_2ede81989ec9c135a1b8506e3552ceab.RData b/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_logs_2ede81989ec9c135a1b8506e3552ceab.RData
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_logs_2ede81989ec9c135a1b8506e3552ceab.rdb b/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_logs_2ede81989ec9c135a1b8506e3552ceab.rdb
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_logs_2ede81989ec9c135a1b8506e3552ceab.rdx b/blogdown/en/sp/spr/spr_run_cache/html/SPRproject_logs_2ede81989ec9c135a1b8506e3552ceab.rdx
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/__packages b/blogdown/en/sp/spr/spr_run_cache/html/__packages
@@ -0,0 +1,18 @@
+base
+BiocStyle
+BiocGenerics
+S4Vectors
+IRanges
+GenomeInfoDb
+GenomicRanges
+XVector
+Biostrings
+Rsamtools
+BiocParallel
+matrixStats
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diff --git a/blogdown/en/sp/spr/spr_run_cache/html/closeR_071fe24a5ada28310e0ef6873ef2f4b6.rdb b/blogdown/en/sp/spr/spr_run_cache/html/closeR_071fe24a5ada28310e0ef6873ef2f4b6.rdb
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/closeR_071fe24a5ada28310e0ef6873ef2f4b6.rdx b/blogdown/en/sp/spr/spr_run_cache/html/closeR_071fe24a5ada28310e0ef6873ef2f4b6.rdx
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diff --git a/blogdown/en/sp/spr/spr_run_cache/html/workflow_bfaba621956993dfadb4d7539b10521b.RData b/blogdown/en/sp/spr/spr_run_cache/html/workflow_bfaba621956993dfadb4d7539b10521b.RData
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/workflow_bfaba621956993dfadb4d7539b10521b.rdb b/blogdown/en/sp/spr/spr_run_cache/html/workflow_bfaba621956993dfadb4d7539b10521b.rdb
diff --git a/blogdown/en/sp/spr/spr_run_cache/html/workflow_bfaba621956993dfadb4d7539b10521b.rdx b/blogdown/en/sp/spr/spr_run_cache/html/workflow_bfaba621956993dfadb4d7539b10521b.rdx
diff --git a/blogdown/md5sum.txt b/blogdown/md5sum.txt
@@ -7,13 +7,15 @@
 "content/en/presentations/sps/SPS_intro.Rmd" "2dffa2488c602e1daaff2edde3eb25ec"
 "content/en/presentations/SPS/SPS_intro.Rmd" "2dffa2488c602e1daaff2edde3eb25ec"
 "content/en/sp/SP_docker.Rmd" "c6f6969d28205d0daa3939f5be85603a"
-"content/en/sp/spr/gettingstarted.Rmarkdown" "70b3bfe2b66f78780046405fd98b437e"
+"content/en/sp/spr/gettingstarted.Rmarkdown" "f2bf3b498d3bc1bd3abc5733f2e40052"
 "content/en/sp/SPR/gettingstarted.Rmarkdown" "f58fbedb6be2b84484cd0707adaf1736"
+"content/en/sp/spr/gettingstarted.Rmd" "f2bf3b498d3bc1bd3abc5733f2e40052"
 "content/en/sp/spr/introduction.Rmarkdown" "db6ccd750b920a509a97fbe8ffdced36"
 "content/en/sp/SPR/introduction.Rmarkdown" "db6ccd750b920a509a97fbe8ffdced36"
-"content/en/sp/spr/SP_docker.Rmd" "5610ea02695b82efb82d765646d6dc3d"
+"content/en/sp/spr/introduction.Rmd" "085ed3391b73e6b4cce1c1a83238b4a5"
+"content/en/sp/spr/SP_docker.Rmd" "bec0e2c81c6e9dac4b3e76366c2b5843"
 "content/en/sp/SPR/SP_docker.Rmd" "5610ea02695b82efb82d765646d6dc3d"
-"content/en/sp/spr/spr_run.Rmarkdown" "f5c82aa80df42ea875b63f68c3479d6d"
+"content/en/sp/spr/spr_run.Rmarkdown" "b6b58d19329135f57f7fb6a07fbf29ad"
 "content/en/sp/SPR/spr_run.Rmarkdown" "f5c82aa80df42ea875b63f68c3479d6d"
 "content/en/sp/spr/SPRinstall.Rmarkdown" "6cd516529bbd80e97f946e6612680b09"
 "content/en/sp/SPR/SPRinstall.Rmarkdown" "6cd516529bbd80e97f946e6612680b09"
@@ -50,7 +52,7 @@
 "content/en/sps/adv_features/config.Rmd" "c17a3384fa17eeb0aba058c7b4a2c983"
 "content/en/sps/adv_features/database.Rmd" "56953d35770c1c1ce4b7320a86a0c65e"
 "content/en/sps/adv_features/debug.Rmd" "0aca84fb178355952987758b38f61593"
-"content/en/sps/adv_features/login.Rmd" "80338a0d44223289b7ac3577f94041e3"
+"content/en/sps/adv_features/login.Rmd" "5a1e78b650081eb8f0f3edc6d2dd42a7"
 "content/en/sps/adv_features/overwritetabs.Rmd" "75850101d8d21cae8613413758c401be"
 "content/en/sps/adv_features/sps_security.Rmd" "ed4993fa7c93789e93c332c52c644303"
 "content/en/sps/adv_features/tabs.Rmarkdown" "fe5d1c5a26323e41ef5ec6acb93e8ecd"

diff --git a/config.toml b/config.toml
@@ -91,7 +91,7 @@ time_format_blog = "2006-01-02"
 # Everything below this are Site Params
 
 [params]
-copyright = "The systemPipeR Project"
+copyright = "The systemPipe Project"
 #privacy_policy = "https://policies.google.com/privacy"
 
 # First one is picked as the Twitter card image if not set on page.
@@ -420,23 +420,23 @@ enable = false
   weight = 3
 ## Training
 [[menu.main]]
-  name = "Training"
+  name = "Outreach"
   weight = 5
-  url = "/training/"
+  url = "/outreach/"
 [[menu.main]]
   name = "Conferences"
   url = "/training/conferences/"
-  parent = "Training"
+  parent = "Outreach"
   weight = 1
 [[menu.main]]
   name = "Presentations"
   url = "/training/presentations/"
-  parent = "Training"
+  parent = "Outreach"
   weight = 2
 [[menu.main]]
   name = "Videos Tutorials"
   url = "/training/videos/"
-  parent = "Training"
+  parent = "Outreach"
   weight = 3
 ## News
 [[menu.main]]
@@ -445,6 +445,11 @@ enable = false
   url = "/News/"
 [[menu.main]]
   name = "Bioconductor 3.12"
-  url = "/news/release_3_12//"
+  url = "/news/release_3_12/"
+  parent = "News"
+  weight = 2
+[[menu.main]]
+  name = "Bioconductor 3.13"
+  url = "/news/release_3_13/"
   parent = "News"
   weight = 1
diff --git a/content/en/about/overview.md b/content/en/about/overview.md
@@ -7,52 +7,35 @@ exclude_search: true
 ---
 
 {{% pageinfo %}}
-Find [here](https://systempipe.org/spr/systempiper_vignette/) all the documentation!
+[systemPipeR](https://systempipe.org/sp/) and [systemPipeShiny](https://systempipe.org/sps/) full documentation!
 {{% /pageinfo %}}
 
-### Motivation
-
-The analysis of Next-generation sequencing (NGS) data remains a 
-major obstacle to the efficient utilization of the technology.  While
-substantial effort has been invested on the development of software dedicated
-to the individual analysis steps of NGS experiments, insufficient resources are
-currently available for integrating the individual software components within
-the widely used R/Bioconductor environment into automated workflows capable of
-running the analysis of most types of NGS applications from start-to-finish in
-a time-efficient and reproducible manner. 
-
-### Results 
-
-To address this need, we have developed the R/Bioconductor package
-_systemPipeR_. It is an extensible environment for both building and
-running end-to-end analysis workflows with automated report generation for a
-wide range of NGS applications. Its unique features include a uniform workflow
-interface across different NGS applications, automated report generation, and 
-support for running both R and command-line software on local computers and
-computer clusters. A flexible sample annotation infrastructure efficiently
-handles complex sample sets and experimental designs.
-
-To simplify the analysis
-of widely used NGS applications, the package provides pre-configured workflows
-and reporting templates for a wide range of NGS applications that are listed on 
-the [Workflow Collection](https://systempipe.org/spr_wf/) 
-page of this site. Additional workflow templates will be provided in the future. _systemPipeR_
-accelerates the extraction of reproducible analysis results from NGS
-experiments. By combining the capabilities of many R/Bioconductor and
-command-line tools, it makes efficient use of existing software resources
-without limiting the user to a set of predefined methods or environments. 
-
-<img align="center" title="spr_overview" src="SPR.png"><img/>
-
-### Availability
-
-_systemPipeR_ is freely available for all common operating systems from
-[Bioconductor](http://bioconductor.org/packages/systemPipeR). Its GitHub 
-repository is [here](https://github.com/tgirke/systemPipeR).
-
-<a href="https://github.com/tgirke/systemPipeR">
-<img align="rigth" title="systemPipeR" src="https://raw.githubusercontent.com/systemPipeR/systemPipeR.github.io/main/static/images/systemPipeR.png" style="width:200px;"><img/>
-</a>
+
+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 align="center" title="systemPipe Project" src="systemPipe_logo.png" style="width:400px;"><img/>
+
+- _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. 
+
+- _systemPipeShiny_ (SPS) integrates a graphical user interface for managing 
+workflows and visualizing results interactively. 
+
+- _systemPipeWorkflow_ (SPW) offers a collection of pre-configured workflow templates.
+
+ ### Availability
+
+All the packages are freely available for all common operating systems from
+[Bioconductor](http://bioconductor.org/packages/systemPipeR). 
+
+- _systemPipeR_ [Bioconductor](http://bioconductor.org/packages/systemPipeR) and [Github](https://github.com/tgirke/systemPipeR)
+
+- _systemPipeShiny_ [Bioconductor](http://bioconductor.org/packages/release/bioc/html/systemPipeShiny.html) and [Github](https://github.com/systemPipeR/systemPipeShiny)
+
+- _systemPipeWorkflow_ [Github](https://github.com/systemPipeR)
 
 ## Acknowledgement
 

diff --git a/content/en/about/overview/systemPipe_logo.png b/content/en/about/overview/systemPipe_logo.png
diff --git a/content/en/news/release_3_12.md b/content/en/news/release_3_12.md
@@ -3,9 +3,10 @@ title: "Bioconductor 3.12"
 linkTitle: "Bioconductor 3.12"
 type: docs
 description: >
+weight: 2
 ---
 
-# *systemPipeR* 1.24 is available
+## *systemPipeR* 1.24 is available
 
 ![image](SYS_WF.png)