Mercurial > repos > mingchen0919 > aurora_dustmasker

diff scripts_generator.sh @ 1:e0828838e0f3 draft default tip
update
author: mingchen0919
date: Fri, 09 Nov 2018 15:25:01 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts_generator.sh	Fri Nov 09 15:25:01 2018 -0500
@@ -0,0 +1,23 @@
+# run SHELL_SCRIPT within tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+
+# generate dustmasker.sh script
+cat >temp.sh <<EOF
+dustmasker \\
+  -in ${X_A} \\
+  -window ${X_B} \\
+  -level ${X_C} \\
+  -linker ${X_D} \\
+  -infmt ${X_E} \\
+  -outfmt ${X_F} \\
+  -parse_seqids ${X_G} \\
+  -out masked_file.txt > dustmasker.log.txt 2>&1
+
+EOF
+
+grep -v 'NO_ARGUMENT_NO' temp.sh > dustmasker.sh
+rm temp.sh
+
+# run dustmasker job
+sh dustmasker.sh
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