Mercurial > repos > dereeper > haplophyle
view Haplophyle.sh @ 2:d6281dc90e20 draft default tip
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author | dereeper |
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date | Wed, 09 Jun 2021 16:54:15 +0000 |
parents | 6f11162b6fa2 |
children |
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#!/bin/bash # Config ####### maxsizeseq=500 maxnumseq=200 ################ tool_path=$(dirname $0) filein=$1 fileout=$2 dotfile=$3 logfile=$4 filein2=$5 groups=$6 nbline=$(sed -n '$=' $filein) let "nbseq = $nbline / 2" seq=$(sed -n 2p $filein) sizeseq=${#seq} if [ $nbseq -lt $maxnumseq ] then if [ $sizeseq -lt $maxsizeseq ] then perl $tool_path/Haplophyle.pl --input $filein --groups $groups --stats $filein2 --dot $dotfile --out $fileout --tool_path $tool_path >>$logfile 2>&1 else echo "Sequence size: $sizeseq" echo "Input Sequences bust have a length < $maxsizeseq" exit 1 fi else echo "$nbseq sequences in the file" echo "Input file must have less than $maxnumseq sequences" exit 1 fi