#!/bin/bash
cat << EOF
inputRedirect = {};
inputRedirect["01"]="Universal"; // genetic code
inputRedirect["02"]="$(readlink -f $1)"; // codon data
inputRedirect["03"]="$(readlink -f $2)"; // tree
inputRedirect["04"]="${3:-All}"; // Test for selection on a branch
inputRedirect["05"]=""; // complete selection


ExecuteAFile (HYPHY_LIB_DIRECTORY+"TemplateBatchFiles/BUSTED.bf", inputRedirect);
EOF

./gen_busted.sh alignment.phy tree.nwk > script.bf

./gen_busted.sh alignment.phy tree.nwk branchLabel > script.bf

HYPHYMP script.bf

HYPHYMP HYPHY_INSTALLATION_PATH/lib/hyphy/TemplateBatchFiles/BUSTED.bf

inputRedirect = {};
inputRedirect["01"]="Universal"; // genetic code
inputRedirect["02"]="/path/to/alignment.phy"; // codon data
inputRedirect["03"]="/path/to/tree.nwk"; // tree
inputRedirect["04"]="All"; // Test for selection on all branches
inputRedirect["05"]="BRANCH1"; // Test for selection on branch1
inputRedirect["06"]="BRANCH2"; // Test for selection on branch2
inputRedirect["07"]=""; // complete selection


ExecuteAFile (HYPHY_LIB_DIRECTORY+"TemplateBatchFiles/BUSTED.bf", inputRedirect);