# HG changeset patch
# User mingchen0919
# Date 1526310001 14400
# Node ID a40d5db8687e1e206ca49770f80e3136adbfc093
# Parent  cf3fde5d08341151dcdcfff0f605a7a030f92980
planemo upload commit 7d411a114317ebd9dfc6a20a7f132e653ccad986-dirty

diff -r cf3fde5d0834 -r a40d5db8687e 01_htseq_count_analysis.Rmd
--- a/01_htseq_count_analysis.Rmd	Tue May 01 11:27:32 2018 -0400
+++ b/01_htseq_count_analysis.Rmd	Mon May 14 11:00:01 2018 -0400
@@ -8,7 +8,7 @@
 ## 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'}
diff -r cf3fde5d0834 -r a40d5db8687e expose-outputs-to-galaxy-history.sh
--- a/expose-outputs-to-galaxy-history.sh	Tue May 01 11:27:32 2018 -0400
+++ b/expose-outputs-to-galaxy-history.sh	Mon May 14 11:00:01 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