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1 #!/bin/bash
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2
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3 # idrPlotWrapper.sh
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4 # OICR: Kar Ming Chu
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5 # July 2012
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6
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7 # BASH wrapper for batch-consistency-plot.r (part of the IDR package)
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8 # For use with Galaxy
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9
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10 # Usage of batch-consistency-plot.r: Rscript batch-consistency-plot-merged.r [npairs] [output.dir] [input.file.prefix 1, 2, 3 ...]
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11 # npairs - will be a constant, since Galaxy requires explicit control over input and output files
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12
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13 # Usage of THIS SCRIPT: ./idrPlotWrapper.sh em uri outputfile
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14 # em - em.sav file provided by Galaxy
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15 # uri - uri.sav file provided by Galaxy
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16 # outputfile - output file name specified by Galaxy
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17
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18 main() {
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19 EM="${1}" # absolute file path to em.sav file, provided by Galaxy
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20 URI="${2}" # absolute file parth to uri.sav file, provided by Galaxy
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21 OUTFILE="${3}" # name of desired output file
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22
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23 cp "${EM}" ./idrPlot-em.sav # cp to this directory and rename so they can be found by idrPlot
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24 cp "${URI}" ./idrPlot-uri.sav
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25
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26 Rscript /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/idr/batch-consistency-plot.r 1 ./idrPlot idrPlot
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27
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28 # convert post script to pdf file
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29 ps2pdf ./idrPlot-plot.ps ./idrPlot-plot.pdf
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30
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31 # rename to output file name
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32 mv ./idrPlot-plot.pdf "${OUTFILE}"
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33
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34 # clean up
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35 rm idrPlot-em.sav
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36 rm idrPlot-uri.sav
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37 }
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38
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39 main "${@}"
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