Mercurial > repos > mingchen0919 > aurora_fastqc_site
diff build-and-run-job-scripts.sh @ 8:94762f1cb779 draft
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
author | mingchen0919 |
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date | Mon, 30 Apr 2018 16:15:39 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build-and-run-job-scripts.sh Mon Apr 30 16:15:39 2018 -0400 @@ -0,0 +1,32 @@ +# run SHELL_SCRIPT within tool outputs directory +cd ${REPORT_FILES_PATH} + +# build job-script.sh +cat >temp.sh <<EOF + +cp ${X_r} read_1.fq +cp ${X_R} read_2.fq + +fastqc \\ + -q \\ + -c ${X_c} \\ + -l ${X_l} \\ + ${X_d}/read_1.fq > read_1.log.txt 2>&1 + +fastqc \\ + -q \\ + -c ${X_c} \\ + -l ${X_l} \\ + ${X_d}/read_2.fq > read_2.log.txt 2>&1 + +EOF + +grep -v None temp.sh > job-1-script.sh +rm temp.sh + +# run SHELL_SCRIPT +sh job-1-script.sh + +# unzip outputs +unzip -q read_1_fastqc.zip +unzip -q read_2_fastqc.zip \ No newline at end of file