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45
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1 #!/bin/bash
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2 random_hash=`date | md5sum | head -c10`
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3 Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads_${random_hash}.stdout 2>/tmp/rnbeads_${random_hash}.stderr
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4 #Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $*
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5 outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"`
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6 echo $outfile
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7 #outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"`
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8
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9
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10 errl=`cat /tmp/rnbeads_${random_hash}.stderr | grep -e "[E|e]rror" | wc -l`
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11 started=`cat /tmp/rnbeads_${random_hash}.stdout | grep -e "STARTED RnBeads Pipeline" | wc -l`
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12 if [ "$started" -lt 1 ]
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13 then
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14 cat /tmp/rnbeads_${random_hash}.stdout >&2
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15 cat /tmp/rnbeads_${random_hash}.stderr >&2
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16 exit 3
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17 else
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18 echo "<html><body>" >> $outfile
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19 echo "<a href=\"index.html\">RnBeads report</a>" >> $outfile
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20 echo "<br/><br/><h5>Output was generated during the execution:</h5><br/>" >> $outfile
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21 echo "<pre>" >> outfile
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22 cat /tmp/rnbeads_${random_hash}.stdout |sed -e "s/$/<br\/>/g" >> $outfile
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23 echo "</pre>" >> outfile
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24 echo "</p>" >> $outfile
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25 echo "</body></html>" >> $outfile
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26 exit 0
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27 fi |
