add package info and tool info to all wf

..Rproj

@@ -0,0 +1,22 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --no-build-vignettes --no-tests
+PackageRoxygenize: rd,collate,namespace

.Rbuildignore

@@ -2,6 +2,6 @@
 ^\.github
 ^docs
 vignettes/*_cache
-
+^\.Rhistory
 ^.*\.Rproj$
 ^\.Rproj\.user$

.gitignore

@@ -8,7 +8,5 @@ docs/articles/systemPipeRIBOseq_files/*
 docs/articles/systemPipeRNAseq_files/*
 docs/articles/systemPipeRdata_files/*
 docs/articles/systemPipeVARseq_files/*
-
-*.Rproj
 .Rproj.user
 .Rhistory

inst/extdata/workflows/chipseq/systemPipeChIPseq.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "ChIP-Seq Workflow Template" 
-author: "Author: Daniela Cassol ([email protected]) and Thomas Girke ([email protected])"
+author: "Author: First Last Name"
 date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" 
 output:
   BiocStyle::html_document:
@@ -141,6 +141,11 @@ sal
 The `systemPipeR` package needs to be loaded [@H_Backman2016-bt].
 
 ```{r load_SPR, message=FALSE, eval=FALSE, spr=TRUE}
+cat(crayon::blue$bold("To use this workflow, following R packages are expected:\n"))
+cat(c("'ggbio", "ChIPseeker", "GenomicFeatures", "GenomicRanges", "Biostrings",
+       "seqLogo", "BCRANK", "readr'\n"), sep = "', '")
+targetspath <- system.file("extdata", "targetsPE_chip.txt", package = "systemPipeR")
+###pre-end
 appendStep(sal) <- LineWise(code = {
                             library(systemPipeR)
                             }, step_name = "load_SPR")
@@ -168,7 +173,7 @@ later, we used the `getColumn` function to extract a named vector.
 ```{r fastq_report, eval=FALSE, message=FALSE, spr=TRUE}
 appendStep(sal) <- LineWise(
     code = {
-        targets <- read.delim("targetsPE_chip.txt", comment.char = "#")
+        targets <- read.delim(targetspath, comment.char = "#")
         updateColumn(sal, step = "load_SPR", position = "targetsWF") <- targets
         fq_files <- getColumn(sal, "load_SPR", "targetsWF", column = 1)
         fqlist <- seeFastq(fastq = fq_files, batchsize = 10000, klength = 8)
@@ -200,7 +205,7 @@ All the parameters are defined on the `preprocessReads-pe.yml` file.
 ```{r preprocessing, message=FALSE, eval=FALSE, spr=TRUE}
 appendStep(sal) <- SYSargsList(
     step_name = "preprocessing",
-    targets = "targetsPE_chip.txt", dir = TRUE,
+    targets = targetspath, dir = TRUE,
     wf_file = "preprocessReads/preprocessReads-pe.cwl",
     input_file = "preprocessReads/preprocessReads-pe.yml",
     dir_path = system.file("extdata/cwl", package = "systemPipeR"),
@@ -292,7 +297,7 @@ to multiple locations. To achieve this, users want to remove the argument settin
 appendStep(sal) <- SYSargsList(
     step_name = "bowtie2_alignment",
     dir = TRUE,
-    targets = "targetsPE_chip.txt",
+    targets = targetspath,
     wf_file = "workflow-bowtie2/workflow_bowtie2-pe.cwl",
     input_file = "workflow-bowtie2/workflow_bowtie2-pe.yml",
     dir_path = system.file("extdata/cwl", package = "systemPipeR"),
@@ -840,13 +845,33 @@ If you are running on a single machine, use following code as an example to chec
 if some tools used in this workflow are in your environment **PATH**. No warning 
 message should be shown if all tools are installed.
 
+## Tools used 
+To check command-line tools used in this workflow, use `listCmdTools`, and use `listCmdModules`
+to check if you have a modular system.
+
+The following code will print out tools required in your custom SPR project in the report. 
+In case you are running the workflow for the first and do not have a project yet, or you 
+just want to browser this workflow, following code displays the tools required by default.
+```{r list_tools}
+if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
+    local({
+        sal <- systemPipeR::SPRproject(resume = TRUE)
+        systemPipeR::listCmdTools(sal)
+        systemPipeR::listCmdModules(sal)
+    })
+} else {
+    cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
+    cat(c("BLAST 2.14.0+"), sep = "\n")
+}
+```
+
+
 ## Session Info
 This is the session information for rendering this report. To access the session information
 of workflow running, check HTML report of `renderLogs`. 
-```{r eval=TRUE}
+```{r report_session_info, eval=TRUE}
 sessionInfo()
 ```
-
 # Funding
 
 This project was supported by funds from the National Institutes of

inst/extdata/workflows/riboseq/systemPipeRIBOseq.Rmd

@@ -1,18 +1,20 @@
 ---
 title: "RIBO-Seq Workflow Template" 
-author: "Author: Daniela Cassol ([email protected]) and Thomas Girke ([email protected])"
+author: "Author: First Last Name"
 date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" 
 output:
   BiocStyle::html_document:
     toc_float: true
     code_folding: show
 package: systemPipeR
 vignette: |
-  %\VignetteIndexEntry{WF: RIBO-Seq Workflow Template}
   %\VignetteEncoding{UTF-8}
+  %\VignetteIndexEntry{WF: RIBO-Seq Workflow Template}
   %\VignetteEngine{knitr::rmarkdown}
 fontsize: 14pt
 bibliography: bibtex.bib
+editor_options: 
+  chunk_output_type: console
 ---
 
 <!--
@@ -194,14 +196,17 @@ sal
 The `systemPipeR` package needs to be loaded [@H_Backman2016-bt].
 
 ```{r load_SPR, message=FALSE, eval=FALSE, spr=TRUE}
+cat(crayon::blue$bold("To use this workflow, following R packages are expected:\n"))
+cat(c("'rtracklayer", "GenomicFeatures", "grid", "BiocParallel", "DESeq2",
+       "ape", "edgeR", "biomaRt", "BBmisc", "pheatmap","ggplot2'\n"), sep = "', '")
+###pre-end
 appendStep(sal) <- LineWise(
     code = {
         library(systemPipeR)
         library(rtracklayer)
         library(GenomicFeatures)
         library(ggplot2)
         library(grid)
-        library(BiocParallel)
         library(DESeq2, quietly=TRUE)
         library(ape, warn.conflicts=FALSE)
         library(edgeR)
@@ -1094,7 +1099,27 @@ making it easier to check any standard output (`stdout`) or standard error
 sal <- renderLogs(sal)
 ```
 
-# Version Information
+## Tools used 
+To check command-line tools used in this workflow, use `listCmdTools`, and use `listCmdModules`
+to check if you have a modular system.
+
+The following code will print out tools required in your custom SPR project in the report. 
+In case you are running the workflow for the first and do not have a project yet, or you 
+just want to browser this workflow, following code displays the tools required by default.
+```{r list_tools}
+if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
+    local({
+        sal <- systemPipeR::SPRproject(resume = TRUE)
+        systemPipeR::listCmdTools(sal)
+        systemPipeR::listCmdModules(sal)
+    })
+} else {
+    cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
+    cat(c("hisat2/2.1.0", "samtools/1.14"), sep = "\n")
+}
+```
+
+## Report  Information
 This is the session information for rendering this report. To access the session information
 of workflow running, check HTML report of `renderLogs`. 
 ```{r sessionInfo_final, eval=TRUE}

inst/extdata/workflows/rnaseq/systemPipeRNAseq.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "RNA-Seq Workflow Template" 
-author: "Author: Daniela Cassol ([email protected]) and Thomas Girke ([email protected])"
+author: "Author: First Last Name"
 date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" 
 output:
   BiocStyle::html_document:
@@ -129,6 +129,10 @@ sal
 The `systemPipeR` package needs to be loaded [@H_Backman2016-bt].
 
 ```{r load_SPR, message=FALSE, eval=FALSE, spr=TRUE}
+cat(crayon::blue$bold("To use this workflow, following R packages are expected:\n"))
+cat(c("'GenomicFeatures", "BiocParallel", "DESeq2",
+       "ape", "edgeR", "biomaRt", "pheatmap","ggplot2'\n"), sep = "', '")
+###pre-end
 appendStep(sal) <- LineWise(code = {
                 library(systemPipeR)
                 }, step_name = "load_SPR")
@@ -636,7 +640,7 @@ appendStep(sal) <- LineWise(
 ![](results/heatmap1.png)
 <div align="center">Figure 6: Heat Map with Hierarchical Clustering Dendrograms of DEGs</div></br>
 
-## Version Information
+## Workflow Information
 
 ```{r sessionInfo, eval=FALSE, spr=TRUE}
 appendStep(sal) <- LineWise(
@@ -724,7 +728,27 @@ making it easier to check any standard output (`stdout`) or standard error
 sal <- renderLogs(sal)
 ```
 
-## Session Info
+## Tools used 
+To check command-line tools used in this workflow, use `listCmdTools`, and use `listCmdModules`
+to check if you have a modular system.
+
+The following code will print out tools required in your custom SPR project in the report. 
+In case you are running the workflow for the first and do not have a project yet, or you 
+just want to browser this workflow, following code displays the tools required by default.
+```{r list_tools}
+if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
+    local({
+        sal <- systemPipeR::SPRproject(resume = TRUE)
+        systemPipeR::listCmdTools(sal)
+        systemPipeR::listCmdModules(sal)
+    })
+} else {
+    cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
+    cat(c("trimmomatic/0.39", "samtools/1.14", "hisat2/2.1.0"), sep = "\n")
+}
+```
+
+## Report Session Info
 This is the session information for rendering this report. To access the session information
 of workflow running, check HTML report of `renderLogs`. 
 ```{r report_session_info, eval=TRUE}

inst/extdata/workflows/varseq/systemPipeVARseq.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "VAR-Seq Workflow Template" 
-author: "Author: Daniela Cassol ([email protected]) and Thomas Girke ([email protected])"
+author: "Author: First Last Name"
 date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" 
 output:
   BiocStyle::html_document:
@@ -143,10 +143,13 @@ The `systemPipeR` package needs to be loaded [@H_Backman2016-bt].
 ```{r load_SPR, message=FALSE, eval=FALSE, spr=TRUE}
 # Some samples in the test dataset do not work well in VARseq, and VARseq workflow 
 # takes long time to process each sample. To better test and speed up the test workflow,
-# sample set is reduced to the first 8 samples.
+# sample set is reduced to the first 13 samples.
 # Please REMOVE the next two lines in your real analysis
 cat(crayon::red$bold("Some samples in targets are removed for test workflow. Please change the template to disable this in your real analysis.\n"))
 writeLines(readLines("targetsPE.txt")[1:13], "targetsPE.txt")
+
+cat(crayon::blue$bold("To use this workflow, following R packages are expected:\n"))
+cat(c("'GenomicFeatures", "VariantAnnotation", "GenomicFeatures", "ggbio", "ggplot2'\n"), sep = "', '")
 ###pre-end
 appendStep(sal) <- LineWise(
     code = {
@@ -957,10 +960,15 @@ appendStep(sal) <- LineWise(
 ![](results/plot_variant.png)
 <div align="center">Figure 3: Plot variants with programmatically.</div></br>
 
-## Version Information
+## Workflow Information
 
-```{r sessionInfo}
-sessionInfo()
+```{r sessionInfo, eval=FALSE, spr=TRUE}
+appendStep(sal) <- LineWise(
+    code = {
+        sessionInfo()
+        }, 
+    step_name = "sessionInfo", 
+    dependency = "plot_variant")
 ```
 
 # Running workflow
@@ -1040,7 +1048,28 @@ making it easier to check any standard output (`stdout`) or standard error
 sal <- renderLogs(sal)
 ```
 
-## Session Info
+## Tools used 
+To check command-line tools used in this workflow, use `listCmdTools`, and use `listCmdModules`
+to check if you have a modular system.
+
+The following code will print out tools required in your custom SPR project in the report. 
+In case you are running the workflow for the first and do not have a project yet, or you 
+just want to browser this workflow, following code displays the tools required by default.
+```{r list_tools}
+if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
+    local({
+        sal <- systemPipeR::SPRproject(resume = TRUE)
+        systemPipeR::listCmdTools(sal)
+        systemPipeR::listCmdModules(sal)
+    })
+} else {
+    cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
+    cat(c("trimmomatic/0.39", "samtools/1.14", "gatk/4.2.0.0", "bcftools/1.15", 
+          "bwa/0.7.17"), sep = "\n")
+}
+```
+
+## Report Session Info
 This is the session information for rendering this report. To access the session information
 of workflow running, check HTML report of `renderLogs`. 
 ```{r report_session_info, eval=TRUE}

vignettes/SPblast.Rmd

@@ -279,7 +279,7 @@ if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
     })
 } else {
     cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
-    cat(c("BLAST 2.14.0+"), sep = "\n")
+    cat(c("bowtie2/2.4.5", "samtools/1.14", "macs2"), sep = "\n")
 }
 ```