Mercurial > repos > mingchen0919 > aurora_fastqc
view build-and-run-job-scripts.sh @ 8:b139968591ee draft default tip
planemo upload commit 9d80f8019f1eb21b0bc6fdb4e3ae7684174f6ca4-dirty
author | mingchen0919 |
---|---|
date | Fri, 30 Nov 2018 19:55:13 -0500 |
parents | 85351cdd4f19 |
children |
line wrap: on
line source
# 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 > /dev/null 2>&1 fastqc \\ -q \\ -c ${X_c} \\ -l ${X_l} \\ ${X_d}/read_2.fq > /dev/null 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