Mercurial > repos > mingchen0919 > aurora_fastqc

diff build-and-run-job-scripts.sh @ 0:0aeed70b3bc5 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author: mingchen0919
date: Fri, 14 Dec 2018 00:38:44 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build-and-run-job-scripts.sh	Fri Dec 14 00:38:44 2018 -0500
@@ -0,0 +1,33 @@
+# 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
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