Mercurial > repos > pavlo-lutsik > rnbeads
comparison rnbeads_galaxy_wrapper.sh @ 21:19b0b536a56f draft
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| author | pavlo-lutsik |
|---|---|
| date | Tue, 02 Jul 2013 14:06:58 -0400 |
| parents | bd8652fa984f |
| children |
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| 20:c423ac1cb9b3 | 21:19b0b536a56f |
|---|---|
| 1 #!/bin/bash | |
| 2 Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads.stdout 2>/tmp/rnbeads.stderr | |
| 3 #Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* | |
| 4 outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"` | |
| 5 echo $outfile | |
| 6 #outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"` | |
| 7 | |
| 8 | |
| 9 if [ -s /tmp/rnbeads.stderr ] | |
| 10 then | |
| 11 cat /tmp/rnbeads.stdout >&2 | |
| 12 #cat $outdir/analysis.log >&2 | |
| 13 cat /tmp/rnbeads.stderr >&2 | |
| 14 exit 3 | |
| 15 else | |
| 16 echo "<html><body>" >> $outfile | |
| 17 echo "<a href=\"index.html\">RnBeads report</a>" >> $outfile | |
| 18 echo "<br/><br/>Output was generated during the execution:<br/>" >> $outfile | |
| 19 echo "<pre>" >> outfile | |
| 20 cat /tmp/rnbeads.stdout |sed -e "s/$/<br\/>/g" >> $outfile | |
| 21 echo "</pre>" >> outfile | |
| 22 echo "</p>" >> $outfile | |
| 23 echo "</body></html>" >> $outfile | |
| 24 exit 0 | |
| 25 fi |