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1 #!/bin/bash
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2 set -e
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3
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4 fasta=$1
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5 library=$2
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6 outputfile=$3
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7 outputmaskedfile=$4
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8 outputlog=$5
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9 outputconfig=$6
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10 outputStats=$7
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11 classif=$8
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12 outputmasked_SSRmaskfile=$9
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13
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14 projectname=$(date "+%Y%m%d")
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15
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16 add=''
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17
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18 if [ -f $classif ]
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19 then
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20 add='-c '$classif
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21 fi
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22
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23 if [ -f $outputStats ]
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24 then
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25 add=$add' -s'
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26 fi
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27
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28 `dirname $0`'/'TEannot_lite.py -i $fasta -l $library -o $outputfile $add > $outputlog
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29 projectname_complete=$(ls $(pwd)|grep $projectname)
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30 working_dir=$(pwd)/$projectname_complete
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31 sed -i 's@'"$working_dir"'@'$projectname'@g' $outputlog
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32 mv $outputfile-$projectname.gff3 $outputfile
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33 mv $outputfile-$projectname.mask $outputmaskedfile
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34 mv $outputfile-$projectname.mask_SSRmask.fa $outputmasked_SSRmaskfile
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35 if [ -f $outputStats ]
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36 then
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37 mv $outputfile-$projectname-TEstats.txt $outputStats
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38 fi
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39
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40 workingconfigfile=$working_dir/TEannot_Galaxy_config_$projectname_complete
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41 sed -i 's|repet_host:.*|repet_host:|g' $workingconfigfile
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42 sed -i 's|repet_user:.*|repet_user:|g' $workingconfigfile
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43 sed -i 's|repet_pw:.*|repet_pw:|g' $workingconfigfile
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44 sed -i 's|repet_db:.*|repet_db:|g' $workingconfigfile
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45 sed -i 's|repet_port:.*|repet_port:|g' $workingconfigfile
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46 sed -i 's|repet_job_manager:.*|repet_job_manager:|g' $workingconfigfile
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47 sed -i 's|project_name:.*|project_name: '$projectname'|g' $workingconfigfile
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48 sed -i 's|project_dir:.*|project_dir:|g' $workingconfigfile
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49 sed -i 's|tmpDir:.*|tmpDir:|g' $workingconfigfile
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50 mv $workingconfigfile $outputconfig
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