# HG changeset patch
# User mingchen0919
# Date 1520183163 18000
# Node ID bcf9ea03aefeacb9b7077459710717ca064de61a
# Parent  5f6352750d820fa09c8400026cfb15b3cd76fffd
working version

diff -r 5f6352750d82 -r bcf9ea03aefe aurora_star_site.sh
--- /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
diff -r 5f6352750d82 -r bcf9ea03aefe aurora_star_site.xml
--- 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
diff -r 5f6352750d82 -r bcf9ea03aefe aurora_star_site_index.Rmd
--- 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
diff -r 5f6352750d82 -r bcf9ea03aefe aurora_star_site_render.R
--- 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
diff -r 5f6352750d82 -r bcf9ea03aefe aurora_star_site_site.yml
--- a/aurora_star_site_site.yml	Sun Mar 04 11:42:48 2018 -0500
+++ b/aurora_star_site_site.yml	Sun Mar 04 12:06:03 2018 -0500
@@ -7,7 +7,7 @@
         - text: "Home"
           icon: fa-home
           href: index.html
-        - text: ""
+        - text: "STAR: RNA-Seq mapping"
           href: aurora_star_site.html
 output:
   html_document: