Mercurial > repos > mingchen0919 > aurora_star_site
changeset 1:bcf9ea03aefe draft
working version
| author | mingchen0919 |
|---|---|
| date | Sun, 04 Mar 2018 12:06:03 -0500 |
| parents | 5f6352750d82 |
| children | 71cbb43b4d91 |
| files | aurora_star_site.sh aurora_star_site.xml aurora_star_site_index.Rmd aurora_star_site_render.R aurora_star_site_site.yml |
| diffstat | 5 files changed, 24 insertions(+), 5 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/aurora_star_site.sh Sun Mar 04 12:06:03 2018 -0500 @@ -0,0 +1,14 @@ +Rscript '${__tool_directory__}/aurora_star_site_render.R' + + -e $echo + -o $report + -d $report.files_path + -s $sink_message + -t '${__tool_directory__}' + + -A '$genomeFastaFiles' + -B '$sjdbGTFfile' + -C '$sjdbOverhang' + -F '$first_reads' + -R '$second_reads' + -S '$sorted_bam' \ No newline at end of file
--- a/aurora_star_site.xml Sun Mar 04 11:42:48 2018 -0500 +++ b/aurora_star_site.xml Sun Mar 04 12:06:03 2018 -0500 @@ -5,7 +5,7 @@ <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="2.5.4a">star</requirement><requirement type="package" version="1.7">samtools</requirement></requirements> <stdio> <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio> - <command><![CDATA[Rscript '${__tool_directory__}/star_render.R' + <command><![CDATA[Rscript '${__tool_directory__}/aurora_star_site_render.R' -e $echo -o $report
--- a/aurora_star_site_index.Rmd Sun Mar 04 11:42:48 2018 -0500 +++ b/aurora_star_site_index.Rmd Sun Mar 04 12:06:03 2018 -0500 @@ -1,5 +1,4 @@ --- -title: "Analysis Report" output: html_document --- @@ -7,5 +6,10 @@ knitr::opts_chunk$set(echo = TRUE, error = TRUE) ``` -## References +# References + +Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6. +Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29. + +Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R (2013). STAR: ultrafast universal RNA-seq aligner. In Bioinformatics, 29 (1), pp. 15--21. \ No newline at end of file
--- a/aurora_star_site_render.R Sun Mar 04 11:42:48 2018 -0500 +++ b/aurora_star_site_render.R Sun Mar 04 12:06:03 2018 -0500 @@ -10,6 +10,7 @@ library(getopt) library(rmarkdown) +library(htmltools) #------------------------------------------------ @@ -55,7 +56,7 @@ #-----------------render site-------------- # copy site generating materials into OUTPUT_DIR dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE) -system(paste0('cp -r ', TOOL_DIR, '/aurora_star_site.Rmd ', OUTPUT_DIR, '/site_generator/skewer.Rmd')) +system(paste0('cp -r ', TOOL_DIR, '/aurora_star_site.Rmd ', OUTPUT_DIR, '/site_generator/aurora_star_site.Rmd')) system(paste0('cp -r ', TOOL_DIR, '/aurora_star_site_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml')) system(paste0('cp -r ', TOOL_DIR, '/aurora_star_site_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd')) # render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file