diff build-and-run-job-scripts.sh @ 1:a110308993be draft

planemo upload for repository https://github.com/feltus/BDSS

--- a/build-and-run-job-scripts.sh	Mon Jun 11 23:04:53 2018 -0400
+++ b/build-and-run-job-scripts.sh	Mon Jun 11 23:40:40 2018 -0400
@@ -1,19 +1,14 @@
 # run job scripts within the tool outputs directory
 cd ${REPORT_FILES_PATH}
+mkdir download_dir
 
-#========== build and run job 1 script ============
-cat >bdss-download.sh <<EOF
-#------------ BELOW IS WHERE YOU WRITE YOUR OWN SHELL SCRIPT --------------
-export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH
+#========== build and run bdss-download.sh script ============
+echo 'export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH' > bdss-download.sh
 
-for $u in $(echo $X_u | sed "s/,/ /g");
-do
-  echo "bdss transfer --destination download_dir -u $u"
-done
-
-
-#------------ END OF SHELL SCRIPT ------------------------------------------  
-EOF
+echo 'for u in $(echo $X_u | sed "s/,/ /g");' >> bdss-download.sh
+echo 'do' >> bdss-download.sh
+echo '  bdss transfer --destination download_dir -u $u' >> bdss-download.sh
+echo 'done' >> bdss-download.sh
 
 
 sh bdss-download.sh