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systemPipeR · Jun 4, 2022 · cba777c · cba777c
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diff --git a/blogdown/md5sum.txt b/blogdown/md5sum.txt
@@ -20,11 +20,19 @@
 "content/en/sp/spr/gettingstarted.Rmd" "41e1512b1a46b70087ebd1707b9d7e5d"
 "content/en/sp/spr/introduction.Rmarkdown" "db6ccd750b920a509a97fbe8ffdced36"
 "content/en/sp/SPR/introduction.Rmarkdown" "db6ccd750b920a509a97fbe8ffdced36"
-"content/en/sp/spr/introduction.Rmd" "e70a53b8905b1ae19a6b2729f0f21279"
+"content/en/sp/spr/introduction.Rmd" "e43b9743306d010a198a11b78660e427"
 "content/en/sp/spr/rnaseq/systemPipeRNAseq_importWF.Rmd" "aca887290afffa359b62db3c188796a2"
 "content/en/sp/spr/rnaseq/systemPipeRNAseq.Rmd" "f4f0af6766f969ef73b9e20f3e14944c"
 "content/en/sp/spr/SP_docker.Rmd" "50a95cf7008fb630d13edc63ad2190a8"
 "content/en/sp/SPR/SP_docker.Rmd" "5610ea02695b82efb82d765646d6dc3d"
+"content/en/sp/spr/sp_run/_index.Rmd" "70528498ede49c651e9ec2bec1624f06"
+"content/en/sp/spr/sp_run/sal_explore.Rmd" "cd9f259bc23033b0c24ecf6d81e3bfb8"
+"content/en/sp/spr/sp_run/step_export.Rmd" "854cd3b26180e78a0a9b49d8af08699a"
+"content/en/sp/spr/sp_run/step_import.Rmd" "62919fee7786ba50c1b3fdfba35277b1"
+"content/en/sp/spr/sp_run/step_interactive.Rmd" "1a4172f1a14fcfa6d46c7ed7d40ab95b"
+"content/en/sp/spr/sp_run/step_reports.Rmd" "0994343e74112d2b3487ac189c16bc19"
+"content/en/sp/spr/sp_run/step_run.Rmd" "79da837c0f1f79820e15fbfd7e59e7c8"
+"content/en/sp/spr/sp_run/step_vis.Rmd" "47b9599adbdc8ae1a4a7e1dd18d51dbe"
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 "content/en/sp/spr/spr_run.Rmd" "9707b3f81d009a1c6c2ef0ed65c411eb"
@@ -33,7 +41,7 @@
 "content/en/sp/spr/steps_oldVersion.Rmd" "254e1e744bbeacbdf9a1ae73f6d27366"
 "content/en/sp/spr/steps.Rmarkdown" "adbba4e2b6b9dc0ea9633a07773db41a"
 "content/en/sp/SPR/steps.Rmarkdown" "449b8b221732c3c94e78af965081c57d"
-"content/en/sp/spr/steps.Rmd" "c33728c05edab401b3cbb4124e5081db"
+"content/en/sp/spr/steps.Rmd" "8d5f3e23cafed5be2fa51749bfa2a529"
 "content/en/sp/spr/steps2.Rmd" "7c3c050a51f148d9ebb08a70976decb8"
 "content/en/sp/spr/templates.Rmarkdown" "498f6995986f6e5c113b7d51212a40ac"
 "content/en/sp/SPR/templates.Rmarkdown" "498f6995986f6e5c113b7d51212a40ac"

diff --git a/content/en/sp/spr/introduction.Rmd b/content/en/sp/spr/introduction.Rmd
@@ -50,7 +50,7 @@ Backman, T.W.H and Girke, T. (2016). _`systemPipeR`_: NGS Workflow and Report Ge
 
 # Introduction
 
-[_`systemPipeR`_](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
+[_`systemPipeR`_(SPR)](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
 provides flexible utilities for designing, building and running automated end-to-end
 analysis workflows for a wide range of research applications, including
 next-generation sequencing (NGS) experiments, such as RNA-Seq, ChIP-Seq,
@@ -130,7 +130,7 @@ and debugging complex workflows from start to finish.
 
 ```{r sysargslistImage, warning= FALSE, eval=TRUE, echo=FALSE, out.width="100%", fig.align = "center", fig.cap= "Workflow steps with input/output file operations are controlled by the _`SYSargsList`_ container. Each of its components (_`SYSargs2`_) are constructed from an optional *targets* and two *param* files. Alternatively, _`LineWise`_ instances containing pure R code can be used."}
 
-knitr::include_graphics("SYSargsList.png")
+knitr::include_graphics("sysargslist.png")
 ```
 
 ## Command-line software support

diff --git a/content/en/sp/spr/introduction.md b/content/en/sp/spr/introduction.md
@@ -1,7 +1,7 @@
 ---
 title: "Introduction" 
 author: "Author: Daniela Cassol (danielac@ucr.edu) and Thomas Girke (thomas.girke@ucr.edu)"
-date: "Last update: 29 April, 2022" 
+date: "Last update: 03 June, 2022" 
 output:
   BiocStyle::html_document:
     toc_float: true
@@ -39,7 +39,7 @@ Backman, T.W.H and Girke, T. (2016). *`systemPipeR`*: NGS Workflow and Report Ge
 
 # Introduction
 
-[*`systemPipeR`*](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
+[*`systemPipeR`*(SPR)](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html)
 provides flexible utilities for designing, building and running automated end-to-end
 analysis workflows for a wide range of research applications, including
 next-generation sequencing (NGS) experiments, such as RNA-Seq, ChIP-Seq,
@@ -128,7 +128,7 @@ and debugging complex workflows from start to finish.
 
 <div class="figure" style="text-align: center">
 
-<img src="SYSargsList.png" alt="Workflow steps with input/output file operations are controlled by the _`SYSargsList`_ container. Each of its components (_`SYSargs2`_) are constructed from an optional *targets* and two *param* files. Alternatively, _`LineWise`_ instances containing pure R code can be used." width="100%" />
+<img src="sysargslist.png" alt="Workflow steps with input/output file operations are controlled by the _`SYSargsList`_ container. Each of its components (_`SYSargs2`_) are constructed from an optional *targets* and two *param* files. Alternatively, _`LineWise`_ instances containing pure R code can be used." width="100%" />
 <p class="caption">
 Figure 3: Workflow steps with input/output file operations are controlled by the *`SYSargsList`* container. Each of its components (*`SYSargs2`*) are constructed from an optional *targets* and two *param* files. Alternatively, *`LineWise`* instances containing pure R code can be used.
 </p>

diff --git a/content/en/sp/spr/rnaseq/.batchtools.conf.R b/content/en/sp/spr/rnaseq/.batchtools.conf.R
@@ -0,0 +1,2 @@
+cluster.functions <- makeClusterFunctionsSlurm(template="batchtools.slurm.tmpl")                      
+
diff --git a/content/en/sp/spr/rnaseq/batchtools.slurm.tmpl b/content/en/sp/spr/rnaseq/batchtools.slurm.tmpl
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+## Job Resource Interface Definition
+##
+## ntasks [integer(1)]:       Number of required tasks,
+##                            Set larger than 1 if you want to further parallelize
+##                            with MPI within your job.
+## ncpus [integer(1)]:        Number of required cpus per task,
+##                            Set larger than 1 if you want to further parallelize
+##                            with multicore/parallel within each task.
+## walltime [integer(1)]:     Walltime for this job, in minutes.
+##                            Must be at least 1 minute.
+## memory   [integer(1)]:     Memory in megabytes for each cpu.
+##                            Must be at least 100 (when I tried lower values my
+##                            jobs did not start at all).
+##
+## Default resources can be set in your .batchtools.conf.R by defining the variable
+## 'default.resources' as a named list.
+
+<%
+# relative paths are not handled well by Slurm
+log.file = normalizePath(log.file, winslash = "/", mustWork = FALSE)
+-%>
+
+
+#SBATCH --job-name=<%= job.name %>
+#SBATCH --output=<%= log.file %>
+#SBATCH --error=<%= log.file %>
+#SBATCH --time=<%= ceiling(resources$walltime / 1) %>
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=<%= resources$ncpus %>
+#SBATCH --mem-per-cpu=<%= resources$memory %>
+<%= if (!is.null(resources$partition)) sprintf(paste0("#SBATCH --partition='", resources$partition, "'")) %>
+<%= if (array.jobs) sprintf("#SBATCH --array=1-%i", nrow(jobs)) else "" %>
+
+## specify which queue on biocluster, one of 'batch', 'highmem', 'intel', 'gpu', 'mygroup'
+##SBATCH -p short 
+##SBATCH -p batch  
+##SBATCH -p intel 
+
+## Initialize work environment like
+## source /etc/profile
+## module add ...
+
+## Export value of DEBUGME environemnt var to slave
+export DEBUGME=<%= Sys.getenv("DEBUGME") %>
+
+## Run R:
+## we merge R output with stdout from SLURM, which gets then logged via --output option
+Rscript -e 'batchtools::doJobCollection("<%= uri %>")'
+