Mercurial > repos > mingchen0919 > aurora_fastqc_site

view build-and-run-job-scripts.sh @ 8:94762f1cb779 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
author mingchen0919
date Mon, 30 Apr 2018 16:15:39 -0400
parents
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 > 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