diff star.Rmd @ 1:44632fc0fc15 draft

update

--- a/star.Rmd	Wed Jun 20 10:24:45 2018 -0400
+++ b/star.Rmd	Wed Jun 20 11:33:55 2018 -0400
@@ -1,5 +1,5 @@
 ---
-title: 'Aurora Tool Report'
+title: 'Aurora STAR Report'
 output:
     html_document:
       highlight: pygments
@@ -55,18 +55,17 @@
 
 
 
-## Job scripts
+```{bash, echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/run-star-jobs.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
+```
 
-```{bash, echo=FALSE}
-sh ${TOOL_INSTALL_DIR}/run-star-jobs.sh
-```
 
 ### Index genome
 
 ```{r echo=FALSE,results='asis'}
 # display content of the job-script.sh file.
 cat('```bash\n')
-cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/1-index-genome.sh')), sep = '\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/scripts/1-index-genome.sh')), sep = '\n')
 cat('\n```')
 ```
 
@@ -75,7 +74,7 @@
 ```{r echo=FALSE,results='asis'}
 # display content of the job-script.sh file.
 cat('```bash\n')
-cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/2-mapping.sh')), sep = '\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/scripts/2-mapping.sh')), sep = '\n')
 cat('\n```')
 ```
 
@@ -84,7 +83,7 @@
 ```{r echo=FALSE,warning=FALSE,results='asis'}
 # display content of the job-script.sh file.
 cat('```bash\n')
-cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/3-sam2bam.sh')), sep = '\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/scripts/3-sam2bam.sh')), sep = '\n')
 cat('\n```')
 ```
 
@@ -93,7 +92,7 @@
 ```{r echo=FALSE,warning=FALSE,results='asis'}
 # display content of the job-script.sh file.
 cat('```bash\n')
-cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/4-flagstat.sh')), sep = '\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/scripts/4-flagstat.sh')), sep = '\n')
 cat('\n```')
 ```
 
@@ -103,6 +102,6 @@
 ```{r echo=FALSE,warning=FALSE,results='asis'}
 # display content of the job-script.sh file.
 cat('```bash\n')
-cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/5-flagstat.txt')), sep = '\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n')
 cat('\n```')
 ```
\ No newline at end of file