--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mgescan.sh	Mon Feb 15 03:33:48 2016 -0500
@@ -0,0 +1,183 @@
+#!/bin/bash
+# mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
+if [ "" == "$MGESCAN_SRC" ]
+then
+	echo "\$MGESCAN_SRC is not defined."
+	exit
+fi
+
+script_program=`which python`
+script=$MGESCAN_SRC/mgescan/cmd.py
+input_file=$1
+#input_file_name=$2
+input_file_name=`basename $input_file`
+hmmsearch_version=$3
+output_file=$4
+program=$5 # N is nonLTR, L is LTR and B is both
+# Optional output parameters for nonLTR
+clade=$6
+en=$7
+rt=$8
+ltr_gff3=$9
+nonltr_gff3=${10}
+both_gff3=${11}
+#### for ltr between $11 and $20
+if [ "$program" == "L" ]
+then
+	sw_rm=${12}
+	scaffold=${13}
+	min_dist=${14}
+	max_dist=${15}
+	min_len_ltr=${16}
+	max_len_ltr=${17}
+	ltr_sim_condition=${18}
+	cluster_sim_condition=${19}
+	len_condition=${20}
+	repeatmasker=${21}
+fi
+
+#elif [ "$program" == "B" ]
+if [ $# -eq 12 ]
+then
+	nmpi=${12}
+	if [ ! -z $nmpi ] && [ $nmpi -ge 1 ]
+	then
+		mpi_enabled="--mpi=$nmpi"
+	fi
+
+fi
+
+# /nfs/nfs4/home/lee212/mgescan/galaxy-dist/tools/mgescan/find_ltr.sh /nfs/nfs4/home/lee212/mgescan/galaxy-dist/database/files/000/dataset_1.dat /nfs/nfs4/home/lee212/mgescan/galaxy-dist/database/files/000/dataset_3.dat
+
+#set path for transeq
+#export PATH=$user_dir/mgescan/EMBOSS/bin:/usr/bin:$PATH
+transeq --version 2> /dev/null
+res=$?
+if [ 0 -ne $res ]
+then
+	echo "EMBOSS is not available."
+	exit
+fi
+
+#move to the working directory
+work_dir=`dirname $script`
+cd $work_dir
+
+#create directory for input and output
+mkdir -p input
+t_dir=`mktemp -p input -d` #relative path
+input_dir="$work_dir/$t_dir/seq" # full path
+output_dir="$work_dir/$t_dir/data"
+mkdir -p $input_dir
+mkdir -p $output_dir
+
+#make a copy of input
+#/bin/cp $input_file $input_dir/$input_file_name
+
+# Check tar.gz
+tar tf $input_file &> /dev/null
+ISGZ=$?
+if [ 0 -eq $ISGZ ]
+then
+	# It seems pre_process.pl creates ./data/genome directory and makes a copy of a genome file.
+	# Due to this reason, extracts compressed inputs to output directory.
+	tar xzf $input_file -C $input_dir 2> /dev/null
+	if [ $? -ne 0 ]
+	then
+		tar xf $input_file -C $input_dir 2> /dev/null
+	fi
+else
+	/bin/ln -s $input_file $input_dir/$input_file_name
+fi
+
+VERSION2=`hmmsearch -h|grep "HMMER 2" 2> /dev/null`
+VERSION3=`hmmsearch -h|grep "HMMER 3" 2> /dev/null`
+if [ "2" == "$hmmsearch_version" ] && [ "" != "$VERSION2" ]
+then
+	echo $VERSION2 selected.
+elif [ "3" == "$hmmsearch_version" ] && [ "" != "$VERSION3" ]
+then
+	echo $VERSION3 selected.
+else
+	echo HMMER is not available.
+	exit
+fi
+
+if [ "$program" == "L" ]
+then
+	program_name="ltr"
+elif [ "$program" == "N" ]
+then
+	program_name="nonltr"
+else
+	program_name="both"
+fi
+
+#run
+$script_program $script $program_name $input_dir/ --output=$output_dir/ $mpi_enabled #-hmmerv=$hmmsearch_version -sw_rm=${11} -scaffold=${12} -min_dist=${13} -max_dist=${14} -min_len_ltr=${15} -max_len_ltr=${16} -ltr_sim_condition=${17} -cluster_sim_condition=${18} -len_condition=${19}
+#/usr/bin/perl $script -genome=$input_dir/ -data=$output_dir/ -hmmerv=$hmmsearch_version -program=$program -sw_rm=${11} -scaffold=${12} -min_dist=${13} -max_dist=${14} -min_len_ltr=${15} -max_len_ltr=${16} -ltr_sim_condition=${17} -cluster_sim_condition=${18} -len_condition=${19}
+
+#RES=`ssh -i $user_dir/.ssh/.internal silo.cs.indiana.edu "/usr/bin/perl $script -genome=$input_dir/ -data=$output_dir/ -hmmerv=$hmmsearch_version -program=$program > /dev/null"`
+
+#make a copy of output
+if [ "$program" != "N" ]
+then
+	/bin/cp $output_dir/ltr/ltr.out $output_file
+	if [ "$ltr_gff3" != "None" ]
+	then
+		/bin/cp $output_dir/ltr/ltr.gff3 $ltr_gff3
+	fi
+
+	if [ "$repeatmasker" != "None" ] && [ "$repeatmasker" != "" ]
+	then
+		# chr2L.fa.cat.gz  chr2L.fa.masked  chr2L.fa.out  chr2L.fa.out.pos  chr2L.fa.tbl
+		/bin/cp $output_dir/repeatmasker/${input_file_name}.out $repeatmasker
+	fi
+fi
+if [ "$program" != "L" ]
+then
+
+	tmp=`mktemp`
+	RANDOM=`basename $tmp`
+	compressed_file=$output_dir/$RANDOM.tar.gz
+	/bin/tar czfP $compressed_file $output_dir/info
+	#/bin/cp $compressed_file $output_file
+	#RES=`/bin/cp $output_dir/info/full/*/* $clade 2> /dev/null`
+	RES=`/bin/cp $compressed_file $clade 2> /dev/null`
+	RES=`/bin/cp $output_dir/info/validation/en $en 2> /dev/null`
+	RES=`/bin/cp $output_dir/info/validation/rt $rt 2> /dev/null`
+	if [ "$nonltr_gff3" != "None" ]
+	then
+		/bin/cp $output_dir/info/nonltr.gff3 $nonltr_gff3
+		# nonltr.gff3
+		##gff-version 3
+		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  19670384        19676921        .       .       .       ID=chr2L.fa_19670384
+		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  17689430        17695994        .       .       .       ID=chr2L.fa_17689430
+		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  11897186        11903717        .       .       .       ID=chr2L.fa_11897186
+		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  49574   56174   .       .       .       ID=chr2L.fa_49574
+	fi
+
+#else
+	# Both LTR, nonLTR executed
+	#compressed_file=$output_dir/$RANDOM.tar.gz
+	#/bin/tar czfP $compressed_file $output_dir
+	#/bin/cp $compressed_file $output_file
+fi
+
+if [ "$program" == "B" ]
+then
+	#echo "track name=LTR description=\"MGEScan-LTR\" color=0,0,255," > $both_gff3
+	/bin/cat $output_dir/ltr/ltr.gff3 >> $both_gff3
+	#echo "track name=nonLTR description=\"MGEScan-nonLTR\" color=255,0,0" >> $both_gff3
+	/bin/cat $output_dir/info/nonltr.gff3 >> $both_gff3
+fi
+
+# delete temp directory
+if [ $? -eq 0 ]
+then
+	rm -rf $work_dir/$t_dir
+	#echo
+else
+	#echo cp -pr $work_dir/$t_dir $work_dir/error-cases/
+	cp -pr $work_dir/$t_dir $work_dir/error-cases/
+fi