--- a/mgescan.sh	Mon Feb 15 01:50:27 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,183 +0,0 @@
-#!/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