Mercurial > repos > mingchen0919 > aurora_deseq2
changeset 29:24a7f1f92db7 draft
planemo upload commit 4a2948a9dd56803572fe5e2d05ff50515ce6d96c-dirty
| author | mingchen0919 |
|---|---|
| date | Fri, 14 Sep 2018 14:03:11 -0400 |
| parents | 27cccfee3018 |
| children | 231de8741468 |
| files | rmarkdown_report.Rmd rmarkdown_report.xml rmarkdown_report_render.R |
| diffstat | 3 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/rmarkdown_report.Rmd Thu Sep 13 15:34:54 2018 -0400 +++ b/rmarkdown_report.Rmd Fri Sep 14 14:03:11 2018 -0400 @@ -9,6 +9,10 @@ knitr::opts_chunk$set(error = TRUE, echo = FALSE) ``` +```{r debug-chunk} +print(1:4) +``` + ```{css echo=FALSE} # code chunks scrollable pre code, pre, code {
--- a/rmarkdown_report.xml Thu Sep 13 15:34:54 2018 -0400 +++ b/rmarkdown_report.xml Fri Sep 14 14:03:11 2018 -0400 @@ -5,7 +5,7 @@ <requirements> <requirement type="package" version="1.15.0.6">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> - <requirement type="package" version="1.3">r-rmarkdown</requirement> + <requirement type="package" version="1.6">r-rmarkdown</requirement> <requirement type="package" version="1.16.1">bioconductor-deseq2</requirement> <requirement type="package" version="4.5.6">r-plotly</requirement> <requirement type="package" version="2.2.1">r-ggplot2</requirement> @@ -25,7 +25,7 @@ export REPORT_FILES_PATH='$report.files_path' && ############ create a hidden file to store r markdown rendering log - touch $report.files_path/.r_rendering.log.txt && + touch $report.files_path/r_rendering.log.txt && ############ finally run the render.R script Rscript '${__tool_directory__}/rmarkdown_report_render.R'
--- a/rmarkdown_report_render.R Thu Sep 13 15:34:54 2018 -0400 +++ b/rmarkdown_report_render.R Fri Sep 14 14:03:11 2018 -0400 @@ -1,7 +1,7 @@ ##============ Sink warnings and errors to a file ============== ## use the sink() function to wrap all code within it. ##============================================================== -zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt')) +zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/r_rendering.log.txt')) sink(zz) sink(zz, type = 'message')