Mercurial > repos > mingchen0919 > aurora_dustmasker
diff scripts_generator.sh @ 1:e0828838e0f3 draft default tip
update
author | mingchen0919 |
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date | Fri, 09 Nov 2018 15:25:01 -0500 |
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--- /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 \ No newline at end of file