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13
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1 #!/bin/bash
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2 Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads.stdout 2>/tmp/rnbeads.stderr
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3 #Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $*
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4 outfile=`echo $* | sed -e "s/.*--output-file=\(.*\)[$[[:blank:]]].*/\1/g"`
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5 outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"`
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6
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7
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8 if [ -s /tmp/rnbeads.stderr ]
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9 then
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10 cat /tmp/rnbeads.stdout >&2
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11 cat $outdir/analysis.log >&2
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12 cat /tmp/rnbeads.stderr >&2
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13 exit 3
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14 else
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15 echo "<html>\n<body>\n" >> $outfile
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16 echo "<a href=\"index.html\">RnBeads report</a>\n" >> $outfile
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17 echo "<br/><br/>\nOutput was generated during the execution:" >> $outfile
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18 echo "<p>" >> outfile
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19 cat /tmp/rnbeads.stdout >> $outfile
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20 echo "</p>" >> $outfile
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21 echo "</body>\n</html>" >> $outfile
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22 exit 0
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23 fi |
