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1 #!/bin/bash
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2 #set -euo pipefail
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3 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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4 echo "protein databases necessary for full clustering analysis"
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5 echo "are downloaded from bitbucket repository using git"
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6 echo ""
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7 cd $DIR
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8 git clone https://bitbucket.org/petrnovak/re_databases.git 2> $DIR/.fetchdb.log
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9 GITEXIT=$?
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10 if [ $GITEXIT -eq "0" ]
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11 then
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12 echo "databases successfully downloaded"
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13 ln -sf $DIR/re_databases/* $DIR/databases/
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14 fi
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15 # cat $DIR/.fetchdb.log
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16 if [ $GITEXIT -eq "128" ]
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17 then
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18 if grep -q -F "Authentication failed" $DIR/.fetchdb.log
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19 then
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20 echo "get login credential from (neumann at umbr.cas.cz)!"
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21 fi
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22 if grep -q -F "already exist" $DIR/.fetchdb.log
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23 then
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24 echo "repository alredy exists, updating..."
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25 cd $DIR/re_databases
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26 git pull && ln -f -s $DIR/re_databases/* $DIR/databases/ && find . -type f -exec touch {} +
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27 fi
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28
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29 fi
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30
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