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3
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1 #!/bin/sh
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2
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3 # Recovering special parameters from crac.xml
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4 ###############################################################
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5 CRAC_BINARY=crac
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6 INDEX_INPUT="$1"
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7
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8 # Getting the indexed genome value
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9 ###############################################################
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10 # Getting the indexed Genome name without the extension
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11 if [ -d "$INDEX_INPUT" ]; then # If $INDEX_INPUT is a directory (that is to say an index from the history)
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12 cpt=0
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13 for fichier in $INDEX_INPUT/*.ssa
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14 do
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15 if [ $((++cpt)) -gt 1 ]; then #More than 1 '.ssa' file is not expected
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16 echo "Warning:Multiple indexes found [$INDEX]" >&2
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17 fi
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18 INDEX=${fichier%%.ssa} #Getting the index from history
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19 done
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20 else
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21 INDEX="$INDEX_INPUT" #Getting the prebuilt index
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22 fi
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23 if [ ! -f "$INDEX.ssa" -a ! -f "$INDEX.conf" ]; then #Both '.ssa' and '.conf' files are required
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24 echo "Error:Index not found [$INDEX]" >&2
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25 exit 1
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26 fi
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27
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28 # Execution of the command line (Submiting job to the cluster)
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29 ###############################################################
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30 shift 2 #Avoiding index_input and output_name.extra_files_path
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31
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32 CRAC_CMD_LINE=""$CRAC_BINARY" -i "$INDEX" "$@""
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33
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34 out=`$CRAC_CMD_LINE`
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35
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36 exit 0
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37
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