From 00cb2b56576c589b223ea6d63a14ca610955bc41 Mon Sep 17 00:00:00 2001
From: John Conklin <jconklin@salk.edu>
Date: Mon, 2 Jun 2025 14:09:12 -0700
Subject: [PATCH] Update working paths

---
 countSummary |  2 +-
 fpkmCluster  |  2 +-
 fpkmPCA      |  2 +-
 justHOMER    | 28 ++++++++++++++--------------
 justSTAR     | 10 +++++-----
 runSTAR      |  2 +-
 6 files changed, 23 insertions(+), 23 deletions(-)
 mode change 100755 => 100644 countSummary
 mode change 100755 => 100644 fpkmCluster
 mode change 100755 => 100644 fpkmPCA
 mode change 100755 => 100644 justHOMER
 mode change 100755 => 100644 justSTAR
 mode change 100755 => 100644 runSTAR

diff --git a/countSummary b/countSummary
old mode 100755
new mode 100644
index 3cbeec9..c80207b
--- a/countSummary
+++ b/countSummary
@@ -1,3 +1,3 @@
 #!/bin/bash
-Rscript /gpfs/tools/scripts/countSummary.R $@
+Rscript /usr/local/share/igc/countSummary.R $@
 
diff --git a/fpkmCluster b/fpkmCluster
old mode 100755
new mode 100644
index cf68940..32473d5
--- a/fpkmCluster
+++ b/fpkmCluster
@@ -1,3 +1,3 @@
 #!/bin/bash
-Rscript /gpfs/tools/scripts/FPKMtoCluster.R $@
+Rscript /usr/local/share/igc/FPKMtoCluster.R $@
 
diff --git a/fpkmPCA b/fpkmPCA
old mode 100755
new mode 100644
index 3047c8f..51f084d
--- a/fpkmPCA
+++ b/fpkmPCA
@@ -1,3 +1,3 @@
 #!/bin/bash
-Rscript /gpfs/tools/scripts/pcaFPKM.R $@
+Rscript /usr/local/share/igc/pcaFPKM.R $@
 
diff --git a/justHOMER b/justHOMER
old mode 100755
new mode 100644
index a984658..9b02c7b
--- a/justHOMER
+++ b/justHOMER
@@ -8,19 +8,19 @@ else
 	GENOME=$1
 	shift 1
 	#justSTAR $GENOME $DIR $@
-	for i in *.sam
-	do
-
-		paired=$(head -n 10000 $i | samtools view -S -f 0x1 - | wc -l)
-		if [[ $paired -gt 0 ]]
-		then
-			echo "Making paired end tag dir: tags/${i%Aligned.out.sam}"
-			makeTagDirectory tags/${i%Aligned.out.sam} $i -sspe -flip 2> ${i%Aligned.out.sam}.tagDirectory.log
-		else
-			echo "Making single end tag dir: tags/${i%Aligned.out.sam}"
-			makeTagDirectory tags/${i%Aligned.out.sam} $i -flip 2> ${i%Aligned.out.sam}.tagDirectory.log
-		fi
-	done 
+#	for i in *.sam
+#	do
+#
+#		paired=$(head -n 10000 $i | samtools view -S -f 0x1 - | wc -l)
+#		if [[ $paired -gt 0 ]]
+#		then
+#			echo "Making paired end tag dir: tags/${i%Aligned.out.sam}"
+#			makeTagDirectory tags/${i%Aligned.out.sam} $i -sspe -flip 2> ${i%Aligned.out.sam}.tagDirectory.log
+#		else
+#			echo "Making single end tag dir: tags/${i%Aligned.out.sam}"
+#			makeTagDirectory tags/${i%Aligned.out.sam} $i -flip 2> ${i%Aligned.out.sam}.tagDirectory.log
+#		fi
+#	done 
 	analyzeRepeats.pl rna ${GENOME} -d tags/* -raw -count exons -condenseGenes -strand + -normMatrix > rawPlus.txt
 	analyzeRepeats.pl rna ${GENOME} -d tags/* -raw -count exons -condenseGenes -strand - -normMatrix > rawMinus.txt
 	plus=$(cat rawPlus.txt | cut -f 9 | tail -n +2 | paste -sd+ | bc)
@@ -41,7 +41,7 @@ else
 	countSummary
 	fpkmCluster
 	fpkmPCA
-	cleanSAMs .
+#	cleanSAMs .
 	echo "done aligning, building tag dirs, quantifying, and making sorted indexed bams"
 	rm -rf *_tmp *_STARtmp
 fi
diff --git a/justSTAR b/justSTAR
old mode 100755
new mode 100644
index 8d5d2e5..7fb3254
--- a/justSTAR
+++ b/justSTAR
@@ -5,7 +5,7 @@ then
 	echo "Usage: runSTAR genomeDir dirWith_R1.fastq.gz [star commands]"
 	echo "Genomes available:"
 
-	genomes=$(ls -d /gpfs/genomes/*.star)
+	genomes=$(ls -d /usr/local/share/igc/genomes/*.star)
 	for i in $genomes
 	do
 		echo ${i##*/}
@@ -14,7 +14,7 @@ else
 	GENOME=$1
 	DIR=$2
 	shift 2
-	STAR --genomeDir /gpfs/genomes/$GENOME --genomeLoad Remove > /dev/null 2> /dev/null
+	STAR --genomeDir /usr/local/share/igc/genomes/$GENOME --genomeLoad Remove > /dev/null 2> /dev/null
 	# first lets combine all of the R1 and R2 reads across lanes and multiple files
 	#for L in $(seq 99)
 	#do
@@ -48,16 +48,16 @@ else
 		if [ -e $R2 ]
 		then
 			echo "Processing paired reads: $R1 and $R2 using genome $GENOME and outputing to $PREFIX"
-			STAR --readFilesCommand zcat --genomeDir /gpfs/genomes/$GENOME --runThreadN 24 --outFilterIntronMotifs RemoveNoncanonical --readFilesIn $R1 $R2 --outFileNamePrefix $PREFIX $@ --genomeLoad LoadAndKeep --outSAMstrandField intronMotif $@ > ${PREFIX}.log
+			STAR --readFilesCommand zcat --genomeDir /usr/local/share/igc/genomes/$GENOME --runThreadN 24 --outFilterIntronMotifs RemoveNoncanonical --readFilesIn $R1 $R2 --outFileNamePrefix $PREFIX $@ --genomeLoad LoadAndKeep --outSAMstrandField intronMotif $@ > ${PREFIX}.log
 		else
 			echo "Processing single-end reads: $R1 using genome $GENOME and outputing to $PREFIX"
-			STAR --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonical  --genomeDir /gpfs/genomes/$GENOME --runThreadN 24 --readFilesIn $R1 --outFileNamePrefix $PREFIX $@ --genomeLoad LoadAndKeep --outSAMstrandField intronMotif $@ > ${PREFIX}.log
+			STAR --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonical  --genomeDir /usr/local/share/igc/genomes/$GENOME --runThreadN 24 --readFilesIn $R1 --outFileNamePrefix $PREFIX $@ --genomeLoad LoadAndKeep --outSAMstrandField intronMotif $@ > ${PREFIX}.log
 		fi
 		end_time="$(date -u +%M)"
 		elapsed="$((10#$end_time-10#$start_time))"
 		echo "Took $elapsed minutes to align $PREFIX"
 	done
-	STAR --genomeDir /gpfs/genomes/$GENOME --genomeLoad Remove > /dev/null
+	STAR --genomeDir /usr/local/share/igc/genomes/$GENOME --genomeLoad Remove > /dev/null
 	rm Aligned.out.sam
 	rm -rf *_tmp *_STARtmp
 fi
diff --git a/runSTAR b/runSTAR
old mode 100755
new mode 100644
index 61fa9d5..d302614
--- a/runSTAR
+++ b/runSTAR
@@ -7,7 +7,7 @@ then
 	echo "set 4th arg if you don't want to run sam to bam conversion at the end (e.g. if you want sams only)"
 	echo "Genomes available:"
 
-	genomes=$(ls -d /gpfs/genomes/*.star)
+	genomes=$(ls -d /usr/local/share/igc/genomes/*.star*)
 	for i in $genomes
 	do
 		echo ${i##*/}