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1 #!/bin/bash
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2
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3
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4 directory=`dirname $0`
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5
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6 if [ -d "$HOME/galaxy_dist/static/images" ]; then
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7 cp -rf $directory/img_sniploid $HOME/galaxy_dist/static/images
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8 fi
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9 if [ -d "$HOME/galaxy-dist/static/images" ]; then
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10 cp -rf $directory/img_sniploid $HOME/galaxy-dist/static/images
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11 fi
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12
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13
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14 if [ "$1" = "poly" ] # poly analysis
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15 then
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16 perl $directory/SNiPloid.pl --dp $2 --dp2 $3 --vp $4 --cpp $5 --vp2 $6 --cpp2 $7 --oc $8 --oh $9 --ohs ${10} --ocs ${11} --elq ${12} --vfp1 ${14} --vfp2 ${15} --img ../../../static/images/img_sniploid/ 2>&1 >>${13}
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17 if [ "${16}" = "yes" ]
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18 then
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19 perl $directory/DrawMapOfOccurences.pl -c ${11} -a ${17} -o ${18} -m 50 -t polyploid_polyploid
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20 fi
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21 elif [ $2 -eq 0 ] # Ref ext
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22 then
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23 perl $directory/SNiPloid.pl --dp $3 --dg1 $4 --vp $5 --cpp $6 --vg1 $7 --cg1 $8 --dg2 $9 --vg2 $10 --cg2 $11 -- ref 0 --oc ${12} --oh ${13} --ohs ${14} --ocs ${15} --elq ${16} --img ../../../static/images/img_sniploid/ 2>&1 >>${17}
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24 else # Ref int == 1
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25 perl $directory/SNiPloid.pl --gn2 $3 --dp $4 --dg1 $5 --vp $6 --cpp $7 --vg1 $8 --cg1 $9 --ref 1 --oc ${10} --oh ${11} --ohs ${12} --ocs ${13} --elq ${14} --img ../../../static/images/img_sniploid/ 2>&1 >>${15}
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26 if [ "${16}" = "yes" ]
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27 then
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28 echo ${16} >>${15}
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29 perl $directory/DrawMapOfOccurences.pl -c ${13} -a ${17} -o ${18} -m 50 -t polyploid_diploid 2>&1 >>${15}
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30 fi
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31 fi
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