Mercurial > repos > pavlo-lutsik > rnbeads
diff rnbeads_galaxy_wrapper.sh @ 45:6b0981ab063e draft default tip
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| author | pavlo-lutsik |
|---|---|
| date | Thu, 14 Aug 2014 14:56:18 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnbeads_galaxy_wrapper.sh Thu Aug 14 14:56:18 2014 -0400 @@ -0,0 +1,27 @@ +#!/bin/bash +random_hash=`date | md5sum | head -c10` +Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads_${random_hash}.stdout 2>/tmp/rnbeads_${random_hash}.stderr +#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* +outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"` +echo $outfile +#outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"` + + +errl=`cat /tmp/rnbeads_${random_hash}.stderr | grep -e "[E|e]rror" | wc -l` +started=`cat /tmp/rnbeads_${random_hash}.stdout | grep -e "STARTED RnBeads Pipeline" | wc -l` +if [ "$started" -lt 1 ] +then + cat /tmp/rnbeads_${random_hash}.stdout >&2 + cat /tmp/rnbeads_${random_hash}.stderr >&2 + exit 3 +else + echo "<html><body>" >> $outfile + echo "<a href=\"index.html\">RnBeads report</a>" >> $outfile + echo "<br/><br/><h5>Output was generated during the execution:</h5><br/>" >> $outfile + echo "<pre>" >> outfile + cat /tmp/rnbeads_${random_hash}.stdout |sed -e "s/$/<br\/>/g" >> $outfile + echo "</pre>" >> outfile + echo "</p>" >> $outfile + echo "</body></html>" >> $outfile + exit 0 +fi \ No newline at end of file