Mercurial > repos > mingchen0919 > aurora_htseq

changeset 14:851112a0071d draft

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planemo upload commit 8758ce271d51387da37298280356fb3f34c4db49-dirty
author mingchen0919
date Mon, 14 May 2018 10:41:39 -0400
parents 650f71d8fc4e
children 70f25691901a
files expose-outputs-to-galaxy-history.sh rmarkdown_report.Rmd
diffstat 2 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/expose-outputs-to-galaxy-history.sh	Tue May 01 11:27:37 2018 -0400
+++ b/expose-outputs-to-galaxy-history.sh	Mon May 14 10:41:39 2018 -0400
@@ -10,4 +10,6 @@
   cp index.html ${REPORT}
 fi
 
-cp count_data.csv ${X_c}
\ No newline at end of file
+if [ -e "count_data.csv" ];then
+  cp count_data.csv ${X_c}
+fi
\ No newline at end of file
--- a/rmarkdown_report.Rmd	Tue May 01 11:27:37 2018 -0400
+++ b/rmarkdown_report.Rmd	Mon May 14 10:41:39 2018 -0400
@@ -56,7 +56,7 @@
 ## Job script
 
 ```{bash, echo=FALSE}
-sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
+sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1
 ```
 
 ```{r echo=FALSE, comment='', results='asis'}