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comparison rnbeads_galaxy_wrapper.sh @ 13:d6cdc73fd57e draft

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author pavlo-lutsik
date Sun, 21 Apr 2013 18:04:11 -0400
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12:73e7d00a9a19 13:d6cdc73fd57e
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 $* | sed -e "s/.*--output-file=\(.*\)[$[[:blank:]]].*/\1/g"`
5 outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"`
6
7
8 if [ -s /tmp/rnbeads.stderr ]
9 then
10 cat /tmp/rnbeads.stdout >&2
11 cat $outdir/analysis.log >&2
12 cat /tmp/rnbeads.stderr >&2
13 exit 3
14 else
15 echo "<html>\n<body>\n" >> $outfile
16 echo "<a href=\"index.html\">RnBeads report</a>\n" >> $outfile
17 echo "<br/><br/>\nOutput was generated during the execution:" >> $outfile
18 echo "<p>" >> outfile
19 cat /tmp/rnbeads.stdout >> $outfile
20 echo "</p>" >> $outfile
21 echo "</body>\n</html>" >> $outfile
22 exit 0
23 fi