Mercurial > repos > pavlo-lutsik > rnbeads
diff rnbeads_galaxy_wrapper.sh @ 13:d6cdc73fd57e draft
Uploaded
| author | pavlo-lutsik |
|---|---|
| date | Sun, 21 Apr 2013 18:04:11 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnbeads_galaxy_wrapper.sh Sun Apr 21 18:04:11 2013 -0400 @@ -0,0 +1,23 @@ +#!/bin/bash +Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads.stdout 2>/tmp/rnbeads.stderr +#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* +outfile=`echo $* | sed -e "s/.*--output-file=\(.*\)[$[[:blank:]]].*/\1/g"` +outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"` + + +if [ -s /tmp/rnbeads.stderr ] +then + cat /tmp/rnbeads.stdout >&2 + cat $outdir/analysis.log >&2 + cat /tmp/rnbeads.stderr >&2 + exit 3 +else + echo "<html>\n<body>\n" >> $outfile + echo "<a href=\"index.html\">RnBeads report</a>\n" >> $outfile + echo "<br/><br/>\nOutput was generated during the execution:" >> $outfile + echo "<p>" >> outfile + cat /tmp/rnbeads.stdout >> $outfile + echo "</p>" >> $outfile + echo "</body>\n</html>" >> $outfile + exit 0 +fi \ No newline at end of file