Mercurial > repos > dereeper > admixture

comparison admixture.sh @ 5:97c9c8daa3c3 draft

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planemo upload
author dereeper
date Wed, 13 Apr 2016 07:51:13 -0400
parents 58df6910f1c3
children
comparison
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4:58df6910f1c3 5:97c9c8daa3c3
6 logs=$5 6 logs=$5
7 best_k_output=$6 7 best_k_output=$6
8 best_k_logfile=$7 8 best_k_logfile=$7
9 kmin=$8 9 kmin=$8
10 kmax=$9 10 kmax=$9
11 groups=${10}
12 threshold_group=${11}
11 13
12 directory=`dirname $0` 14 directory=`dirname $0`
13 mkdir tmpdir$$ 15 mkdir tmpdir$$
14 cp -rf $bed tmpdir$$/input.bed 16 cp -rf $bed tmpdir$$/input.bed
15 cp -rf $fam tmpdir$$/input.fam 17 cp -rf $fam tmpdir$$/input.fam
16 cp -rf $bim tmpdir$$/input.bim 18 cp -rf $bim tmpdir$$/input.bim
17 19
18 20
19 perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ 21 perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ -t $threshold_group
20 22
21 mv tmpdir$$/output $best_k_output 23 mv tmpdir$$/output $best_k_output
22 mv tmpdir$$/log $best_k_logfile 24 mv tmpdir$$/log $best_k_logfile
23 mv tmpdir$$/outputs.Q $outputs 25 mv tmpdir$$/outputs.Q $outputs
24 mv tmpdir$$/logs $logs 26 mv tmpdir$$/logs $logs
27 mv tmpdir$$/groups $groups
25 28
26 29