update gatk

NYU-Molecular-Pathology · Aug 7, 2017 · 9c02efc · 9c02efc
1 parent f4776b8
commit 9c02efc
Show file tree

Hide file tree

Showing 7 changed files with 7 additions and 7 deletions.
diff --git a/run b/run
@@ -128,7 +128,7 @@ sub run_samples {
 	chomp(@unique_samples);
 
 	# check that sample names do not contain problematic characters
-	my @invalid_samples = grep(/[^\w\-\.]/, @unique_samples);
+	my @invalid_samples = grep(/[^\w\-\.\:]/, @unique_samples);
 	if (@invalid_samples) {
 		my $invalid_samples_str = join(', ', @invalid_samples);
 		die "\n\n ERROR: SAMPLES $invalid_samples_str CONTAIN PROBLEMATIC CHARACTERS \n\n";

diff --git a/segments/bam-ra-rc-gatk.sh b/segments/bam-ra-rc-gatk.sh
@@ -129,7 +129,7 @@ module load r/3.3.0
 module unload zlib
 
 # command
-gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar"
+gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar"
 gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}"
 
 if [ ! -s "$gatk_jar" ] ; then

diff --git a/segments/bam-splitncigar-gatk.sh b/segments/bam-splitncigar-gatk.sh
@@ -99,7 +99,7 @@ module load java/1.8
 module load r/3.3.0
 
 # command
-gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar"
+gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar"
 gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}"
 
 if [ ! -s "$gatk_jar" ] ; then

diff --git a/segments/qc-coverage-gatk.sh b/segments/qc-coverage-gatk.sh
@@ -100,7 +100,7 @@ module unload java
 module load java/1.8
 
 # command
-gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar"
+gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar"
 gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}"
 
 if [ ! -s "$gatk_jar" ] ; then

diff --git a/segments/qc-target-reads-gatk.sh b/segments/qc-target-reads-gatk.sh
@@ -104,7 +104,7 @@ module unload java
 module load java/1.8
 
 # command
-gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar"
+gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar"
 gatk_cmd="java -Xms16G -Xmx16G -jar $gatk_jar"
 
 gatk_omit_arg="--omitIntervalStatistics --omitLocusTable --omitDepthOutputAtEachBase"

diff --git a/segments/snvs-gatk-hc.sh b/segments/snvs-gatk-hc.sh
@@ -96,7 +96,7 @@ module unload java
 module load java/1.8
 
 # command
-gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar"
+gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar"
 gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}"
 
 # error log (DEBUG, INFO (default), WARN, ERROR, FATAL, OFF)

diff --git a/segments/snvs-mutect2.sh b/segments/snvs-mutect2.sh
@@ -111,7 +111,7 @@ module unload java
 module load java/1.8
 
 # command
-gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar"
+gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar"
 gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}"
 
 if [ ! -s "$gatk_jar" ] ; then