diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index c955ce36531..658502adf59 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -17,7 +17,7 @@
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "CountCovariates"
-    --num_threads 4 ##hard coded, for now
+    --num_threads \${GALAXY_SLOTS:-4}
     -et "NO_ET" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 853ab8f24cb..58b6c86dc05 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -19,7 +19,7 @@
     -T "RealignerTargetCreator"
     -o "${output_interval}"
     -et "NO_ET" ##ET no phone home
-    --num_threads 4 ##hard coded, for now
+    --num_threads \${GALAXY_SLOTS:-4}
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 39d095cca97..c54e7b1b08b 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -19,7 +19,7 @@
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "UnifiedGenotyper"
-    --num_threads 4 ##hard coded, for now
+    --num_threads \${GALAXY_SLOTS:-4}
     --out "${output_vcf}"
     --metrics_file "${output_metrics}"
     -et "NO_ET" ##ET no phone home
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 5055eed3fca..bd036254a13 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -17,7 +17,7 @@
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "VariantEval"
     --out "${output_report}"
-    --num_threads 4 ##hard coded, for now
+    --num_threads \${GALAXY_SLOTS:-4}
     -et "NO_ET" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 7aa3c94b293..e1d2513ff7c 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -15,7 +15,7 @@
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "VariantRecalibrator"
-    --num_threads 4 ##hard coded, for now
+    --num_threads \${GALAXY_SLOTS:-4}
     -et "NO_ET" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
diff --git a/tools/gatk/variant_select.xml b/tools/gatk/variant_select.xml
index 973469f503c..4c14793c657 100644
--- a/tools/gatk/variant_select.xml
+++ b/tools/gatk/variant_select.xml
@@ -14,7 +14,7 @@
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "SelectVariants"
-    --num_threads 4 ##hard coded, for now
+    --num_threads \${GALAXY_SLOTS:-4}
     -et "NO_ET" ##ET no phone home
     -o "${output_vcf}"