Mercurial > repos > pavlo-lutsik > rnbeads
comparison rnbeads_galaxy_wrapper.sh @ 35:25209b26dc76 draft
Uploaded
| author | pavlo-lutsik |
|---|---|
| date | Fri, 05 Jul 2013 09:03:12 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 34:0a295cbbfe69 | 35:25209b26dc76 |
|---|---|
| 1 #!/bin/bash | |
| 2 random_hash=`tr -dc "[:alpha:]" < /dev/urandom | head -c 8` | |
| 3 Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads_${random_hash}.stdout 2>/tmp/rnbeads_${random_hash}.stderr | |
| 4 #Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* | |
| 5 outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"` | |
| 6 echo $outfile | |
| 7 #outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"` | |
| 8 | |
| 9 | |
| 10 errl=`cat /tmp/rnbeads.stderr | grep -e "[E|e]rror" | wc -l` | |
| 11 if [ "$errl" -gt 0 ] | |
| 12 then | |
| 13 cat /tmp/rnbeads.stdout >&2 | |
| 14 #cat $outdir/analysis.log >&2 | |
| 15 cat /tmp/rnbeads.stderr >&2 | |
| 16 exit 3 | |
| 17 else | |
| 18 echo "<html><body>" >> $outfile | |
| 19 echo "<a href=\"index.html\">RnBeads report</a>" >> $outfile | |
| 20 echo "<br/><br/>Output was generated during the execution:<br/>" >> $outfile | |
| 21 echo "<pre>" >> outfile | |
| 22 cat /tmp/rnbeads.stdout |sed -e "s/$/<br\/>/g" >> $outfile | |
| 23 echo "</pre>" >> outfile | |
| 24 echo "</p>" >> $outfile | |
| 25 echo "</body></html>" >> $outfile | |
| 26 exit 0 | |
| 27 fi |