update scripts

Kingsford-Group · Apr 13, 2017 · 8e77611 · 8e77611
1 parent a2b6cd9
commit 8e77611
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Showing 8 changed files with 197 additions and 3 deletions.
diff --git a/bin/run.encode10.sh b/bin/run.encode10.sh
@@ -11,6 +11,41 @@ do
 	esac
 done
 
+
+bin=`pwd`/../programs
+gtf=`pwd`/../data/ensembl
+
+if [ ! -x $bin/scallop ]; then
+	echo "please make sure $bin/scallop is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/stringtie ]; then
+	echo "please make sure $bin/stringtie is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/transcomb ]; then
+	echo "please make sure $bin/transcomb is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
+if [ ! -s $gtf/GRCh38.gtf ]; then
+	echo "please make sure $gtf/GRCh38.gtf is available (you may run ./download.annotation.sh)"
+	exit
+fi
+
+if [ ! -s $gtf/GRCh37.gtf ]; then
+	echo "please make sure $gtf/GRCh37.gtf is available (you may run ./download.annotation.sh)"
+	exit
+fi
+
+
 nohup ./run.scallop.encode10.sh -c $coverage &
 nohup ./run.stringtie.encode10.sh -c $coverage &
 nohup ./run.transcomb.encode10.sh -c $coverage &
diff --git a/bin/run.encode65.sh b/bin/run.encode65.sh
@@ -2,7 +2,7 @@
 
 coverage="default"
 
-while getopts "c:p:" arg
+while getopts "c:" arg
 do
 	case $arg in 
 	c) 
@@ -11,6 +11,38 @@ do
 	esac
 done
 
+bin=$dir/../programs
+
+if [ ! -x $bin/scallop ]; then
+	echo "please make sure $bin/scallop is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/stringtie ]; then
+	echo "please make sure $bin/stringtie is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/transcomb ]; then
+	echo "please make sure $bin/transcomb is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
+if [ ! -s $gtf/GRCh38.gtf ]; then
+	echo "please make sure $gtf/GRCh38.gtf is available (you may run ./download.annotation.sh)"
+	exit
+fi
+
+if [ ! -s $gtf/GRCh37.gtf ]; then
+	echo "please make sure $gtf/GRCh37.gtf is available (you may run ./download.annotation.sh)"
+	exit
+fi
+
 nohup ./run.scallop.encode65.sh -c $coverage &
 nohup ./run.stringtie.encode65.sh -c $coverage &
 nohup ./run.transcomb.encode65.sh -c $coverage &
diff --git a/bin/run.scallop.encode10.sh b/bin/run.scallop.encode10.sh
@@ -14,6 +14,16 @@ done
 dir=`pwd`
 bin=$dir/../programs
 
+if [ ! -x $bin/scallop ]; then
+	echo "please make sure $bin/scallop is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
 list=$dir/encode10.list
 datadir=$dir/../data/encode10
 results=$dir/../results/encode10
@@ -27,9 +37,20 @@ do
 	gm=`echo $x | cut -f 3 -d ":"`
 	gtf=$dir/../data/ensembl/$gm.gtf
 
+	if [ ! -s $gtf ]; then
+		echo "make sure $gtf is available"
+		exit
+	fi
+
 	for aa in `echo "tophat star hisat"`
 	do
 		bam=$datadir/$id/$aa.sort.bam
+
+		if [ ! -s $bam ]; then
+			echo "make sure $bam is available"
+			exit
+		fi
+
 		cur=$results/$id.$aa/scallop.$coverage
 		mkdir -p $cur
 

diff --git a/bin/run.scallop.encode65.sh b/bin/run.scallop.encode65.sh
@@ -14,6 +14,16 @@ done
 dir=`pwd`
 bin=$dir/../programs
 
+if [ ! -x $bin/scallop ]; then
+	echo "please make sure $bin/scallop is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
 list=$dir/encode65.list
 datadir=$dir/../data/encode65
 results=$dir/../results/encode65
@@ -26,8 +36,18 @@ do
 	ss=`echo $x | cut -f 2 -d ":"`
 	gm=`echo $x | cut -f 3 -d ":"`
 	gtf=$dir/../data/ensembl/$gm.gtf
-
 	bam=$datadir/$id.bam
+
+	if [ ! -s $gtf ]; then
+		echo "make sure $gtf is available"
+		exit
+	fi
+
+	if [ ! -s $bam ]; then
+		echo "make sure $bam is available"
+		exit
+	fi
+
 	cur=$results/$id/scallop.$coverage
 	mkdir -p $cur
 

diff --git a/bin/run.stringtie.encode10.sh b/bin/run.stringtie.encode10.sh
@@ -14,6 +14,17 @@ done
 dir=`pwd`
 bin=$dir/../programs
 
+if [ ! -x $bin/stringtie ]; then
+	echo "please make sure $bin/stringtie is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
+
 list=$dir/encode10.list
 datadir=$dir/../data/encode10
 results=$dir/../results/encode10
@@ -27,6 +38,11 @@ do
 	gm=`echo $x | cut -f 3 -d ":"`
 	gtf=$dir/../data/ensembl/$gm.gtf
 
+	if [ ! -s $gtf ]; then
+		echo "make sure $gtf is available"
+		exit
+	fi
+
 	st="";
 	if [ "$ss" == "first" ]; then
 		st="--rf"
@@ -37,6 +53,12 @@ do
 	for aa in `echo "tophat star hisat"`
 	do
 		bam=$datadir/$id/$aa.sort.bam
+
+		if [ ! -s $bam ]; then
+			echo "make sure $bam is available"
+			exit
+		fi
+
 		cur=$results/$id.$aa/stringtie.$coverage
 		mkdir -p $cur
 

diff --git a/bin/run.stringtie.encode65.sh b/bin/run.stringtie.encode65.sh
@@ -14,6 +14,17 @@ done
 dir=`pwd`
 bin=$dir/../programs
 
+if [ ! -x $bin/stringtie ]; then
+	echo "please make sure $bin/stringtie is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
+
 list=$dir/encode65.list
 datadir=$dir/../data/encode65
 results=$dir/../results/encode65
@@ -27,6 +38,17 @@ do
 	gm=`echo $x | cut -f 3 -d ":"`
 
 	gtf=$dir/../data/ensembl/$gm.gtf
+	bam=$datadir/$id.bam
+
+	if [ ! -s $gtf ]; then
+		echo "make sure $gtf is available"
+		exit
+	fi
+
+	if [ ! -s $bam ]; then
+		echo "make sure $bam is available"
+		exit
+	fi
 
 	st="";
 	if [ "$ss" == "first" ]; then
@@ -35,7 +57,6 @@ do
 		st="--fr"
 	fi
 
-	bam=$datadir/$id.bam
 	cur=$results/$id/stringtie.$coverage
 	mkdir -p $cur
 

diff --git a/bin/run.transcomb.encode10.sh b/bin/run.transcomb.encode10.sh
@@ -14,6 +14,17 @@ done
 dir=`pwd`
 bin=$dir/../programs
 
+if [ ! -x $bin/transcomb ]; then
+	echo "please make sure $bin/transcomb is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
+
 list=$dir/encode10.list
 datadir=$dir/../data/encode10
 results=$dir/../results/encode10
@@ -27,9 +38,20 @@ do
 	gm=`echo $x | cut -f 3 -d ":"`
 	gtf=$dir/../data/ensembl/$gm.gtf
 
+	if [ ! -s $gtf ]; then
+		echo "make sure $gtf is available"
+		exit
+	fi
+
 	for aa in `echo "tophat star hisat"`
 	do
 		bam=$datadir/$id/$aa.sort.bam
+
+		if [ ! -s $bam ]; then
+			echo "make sure $bam is available"
+			exit
+		fi
+
 		cur=$results/$id.$aa/transcomb.$coverage
 		mkdir -p $cur
 

diff --git a/bin/run.transcomb.encode65.sh b/bin/run.transcomb.encode65.sh
@@ -14,6 +14,16 @@ done
 dir=`pwd`
 bin=$dir/../programs
 
+if [ ! -x $bin/transcomb ]; then
+	echo "please make sure $bin/transcomb is available/executable"
+	exit
+fi
+
+if [ ! -x $bin/gffcompare ]; then
+	echo "please make sure $bin/gffcompare is available/executable"
+	exit
+fi
+
 list=$dir/encode65.list
 datadir=$dir/../data/encode65
 results=$dir/../results/encode65
@@ -28,6 +38,17 @@ do
 
 	gtf=$dir/../data/ensembl/$gm.gtf
 	bam=$datadir/$id.bam
+
+	if [ ! -s $gtf ]; then
+		echo "make sure $gtf is available"
+		exit
+	fi
+
+	if [ ! -s $bam ]; then
+		echo "make sure $bam is available"
+		exit
+	fi
+
 	cur=$results/$id/transcomb.$coverage
 	mkdir -p $cur