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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 outputfasta=$2
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6 classif=$3
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7 outputlog=$4
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8 outputclassif=$7
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9 outputconfig=$5
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10 outputstats=$6
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11
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12 projectname=$(date "+%Y%m%d")
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13
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14
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15 add=''
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16
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17 if [ $classif == yes ]
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18 then
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19 add='-c'
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20 fi
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21 `dirname $0`'/'TEdenovo_lite.py -i $fasta -o $outputfasta $add > $outputlog
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22 projectname_complete=$(ls $(pwd)|grep $projectname)
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23 working_dir=$(pwd)/$projectname_complete
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24 sed -i 's@'"$working_dir"'@'$projectname'@g' $outputlog
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25 mv $outputfasta-$projectname-denovoLibTEs_filtered.fa $outputfasta
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26 mv $outputfasta-$projectname-classif_stats.txt $outputstats
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27 if [ $classif == yes ]
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28 then
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29 mv $outputfasta-$projectname.classif $outputclassif
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30 fi
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31
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32
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33 workingconfigfile=$working_dir/TEdenovo_Galaxy_config_$projectname_complete
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34 sed -i 's|repet_host:.*|repet_host:|g' $workingconfigfile
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35 sed -i 's|repet_user:.*|repet_user:|g' $workingconfigfile
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36 sed -i 's|repet_pw:.*|repet_pw:|g' $workingconfigfile
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37 sed -i 's|repet_db:.*|repet_db:|g' $workingconfigfile
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38 sed -i 's|repet_port:.*|repet_port:|g' $workingconfigfile
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39 sed -i 's|repet_job_manager:.*|repet_job_manager:|g' $workingconfigfile
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40 sed -i 's|project_name:.*|project_name: '$projectname'|g' $workingconfigfile
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41 sed -i 's|project_dir:.*|project_dir:|g' $workingconfigfile
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42 sed -i 's|tmpDir:.*|tmpDir:|g' $workingconfigfile
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43 mv $workingconfigfile $outputconfig
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44
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