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1 #!/bin/sh
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2
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3 #------------------------------------------------------------------------------
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4 # Create a zip file for distribution
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5 # Note: Only binary data is included (no raw gene info / genomes)
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6 #
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7 # Pablo Cingolani 2010
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8 #------------------------------------------------------------------------------
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9
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10 VERSION="2_1"
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11 VERSION_REV=$VERSION"a"
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12 DIR=$HOME/snpEff_$VERSION_REV
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13 rm -rvf $DIR
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14 mkdir $DIR
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15
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16 # Copy core files
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17 cp snpEff.config snpEff.jar $DIR
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18 cp -rvfH galaxy scripts $DIR
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19
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20 cd $DIR
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21 rm -rvf `find . -name "CVS" -type d`
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22 cd -
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23
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24 # Create 'core' zip file
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25 cd $HOME
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26 ZIP="snpEff_v"$VERSION_REV"_core.zip"
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27 rm -f $ZIP 2> /dev/null
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28 zip -r $ZIP snpEff_$VERSION_REV
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29 cd -
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30
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31 # Create ZIP file for each database
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32 for d in `ls data/*/snpEffectPredictor.bin`
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33 do
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34 DIR=`dirname $d`
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35 GEN=`basename $DIR`
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36
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37 echo $GEN
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38 ZIP="snpEff_v"$VERSION"_"$GEN".zip"
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39 zip -r $ZIP data/$GEN/*.bin
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40 done
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41
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42 # Look for missing genomes
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43 echo Missing genomes:
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44 ls -d data/*/snpEffectPredictor.bin | grep -v genomes | cut -f 2 -d / | sort > genomes_bins.txt
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45 ls -d data/* | grep -v genomes | cut -f 2 -d / | sort > genomes_dirs.txt
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46 diff genomes_dirs.txt genomes_bins.txt | grep "^<"
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47
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