Mercurial > repos > mingchen0919 > aurora_fastqc_site

diff build-and-run-job-scripts.sh @ 8:94762f1cb779 draft
planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
author: mingchen0919
date: Mon, 30 Apr 2018 16:15:39 -0400
--- /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