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01_StartOpsinProcessing.sh
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01_StartOpsinProcessing.sh
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#!/bin/bash
# Get the directory where this script is
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
thisScript="$(basename "$(test -L "$0" && readlink "$0" || echo "$0")")"
gene=$(basename "$DIR")
bigTreeIteration="10" # Actually this is the default
bigNumRoundsLeft="10" # Actually this is the default
aligner="PASTA" # Is the default
#continue="" # No default
continue="--continue" # No default
numRoundsLeft="20" # Is the default
shuffleSeqs="--shuffleSeqs" # Shuffle the sequences between iterations of Rogue removal, this should be done
extension="contree" # Extension of tree files to extract the sequences of interests from
trimAl="Default" # Value for trimAl use Default value, values are between 0.0 and 1.0, default is 0.1.
"$DIR/../PhylogenyPipeline/Scheduler/Scheduler-01-PrepareSequences.sh" -g $gene -b $bigTreeIteration -a $aligner $continue -n $numRoundsLeft -N $bigNumRoundsLeft $shuffleSeqs -e $extension -t $trimAl