Mercurial > repos > dereeper > admixture
comparison admixture.sh @ 4:58df6910f1c3 draft
planemo upload
| author | dereeper |
|---|---|
| date | Tue, 12 Apr 2016 09:31:56 -0400 |
| parents | |
| children | 97c9c8daa3c3 |
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| 3:9f6977aae93a | 4:58df6910f1c3 |
|---|---|
| 1 #!/bin/bash | |
| 2 bed=$1 | |
| 3 fam=$2 | |
| 4 bim=$3 | |
| 5 outputs=$4 | |
| 6 logs=$5 | |
| 7 best_k_output=$6 | |
| 8 best_k_logfile=$7 | |
| 9 kmin=$8 | |
| 10 kmax=$9 | |
| 11 | |
| 12 directory=`dirname $0` | |
| 13 mkdir tmpdir$$ | |
| 14 cp -rf $bed tmpdir$$/input.bed | |
| 15 cp -rf $fam tmpdir$$/input.fam | |
| 16 cp -rf $bim tmpdir$$/input.bim | |
| 17 | |
| 18 | |
| 19 perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ | |
| 20 | |
| 21 mv tmpdir$$/output $best_k_output | |
| 22 mv tmpdir$$/log $best_k_logfile | |
| 23 mv tmpdir$$/outputs.Q $outputs | |
| 24 mv tmpdir$$/logs $logs | |
| 25 | |
| 26 |