--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mgescan.sh	Sat Jun 14 19:06:49 2014 -0400
@@ -0,0 +1,126 @@
+#!/bin/bash
+# mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
+user_dir=/u/lee212
+#script=$user_dir/retrotminer/wazim/MGEScan1.1/run_MGEScan.pl
+#script=$user_dir/retrotminer/wazim/MGEScan1.3.1/run_MGEScan2.pl
+source $user_dir/virtualenv/retrotminer/bin/activate
+script_program=`which python`
+script=$user_dir/github/retrotminer/retrotminer/retrotminer.py
+input_file=$1
+input_file_name=$2
+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}
+#### for ltr between $11 and $20
+sw_rm=${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}
+repeatmasker=${20}
+
+# /nfs/nfs4/home/lee212/retrotminer/galaxy-dist/tools/retrotminer/find_ltr.sh /nfs/nfs4/home/lee212/retrotminer/galaxy-dist/database/files/000/dataset_1.dat /nfs/nfs4/home/lee212/retrotminer/galaxy-dist/database/files/000/dataset_3.dat
+
+#load env?
+source $user_dir/.bashrc
+source $user_dir/.bash_profile
+
+#set path for transeq
+export PATH=$user_dir/retrotminer/EMBOSS/bin:/usr/bin:$PATH
+
+#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
+
+if [ "2" == "$hmmsearch_version" ]
+then
+	export PATH=$user_dir/retrotminer/HMMER2.0/bin:$PATH
+else
+	export PATH=/usr/bin:$PATH
+fi
+
+if [ "$program" == "L" ]
+then
+	program_name="ltr"
+else
+	programname="nonltr"
+fi
+
+#run
+$script_program $script $program_name $input_dir/ --output=$output_dir/ #-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" ]
+	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
+
+	#compressed_file=$output_dir/$RANDOM.tar.gz
+	#/bin/tar cvzfP $compressed_file $output_dir/info
+	#/bin/cp $compressed_file $output_file
+	/bin/cp $output_dir/info/full/*/* $clade
+	/bin/cp $output_dir/info/validation/en $en
+	/bin/cp $output_dir/info/validation/rt $rt
+	if [ "$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 cvzfP $compressed_file $output_dir
+	#/bin/cp $compressed_file $output_file
+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