# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1347590444 18000
# Node ID ebe280eca4a4d40c9f7b48b3387af69c7264a23a
# Parent  388f178f9e13c743f9bcf610ba1283ab89d08eea
Add package requirement

diff -r 388f178f9e13 -r ebe280eca4a4 snpEff.xml
--- a/snpEff.xml	Thu Sep 13 22:33:33 2012 -0400
+++ b/snpEff.xml	Thu Sep 13 21:40:44 2012 -0500
@@ -6,6 +6,7 @@
 	<command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
 	-->
 	<requirements>
+		<requirement type="package" version="3.0f">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>java -Xmx6G -jar $JAVA_JAR_PATH/snpEff.jar eff -c $JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
diff -r 388f178f9e13 -r ebe280eca4a4 snpEff_download.xml
--- a/snpEff_download.xml	Thu Sep 13 22:33:33 2012 -0400
+++ b/snpEff_download.xml	Thu Sep 13 21:40:44 2012 -0500
@@ -1,6 +1,7 @@
 <tool id="snpEff_download" name="SnpEff Download" version="1.0">
 	<description>Download a new database</description>
 	<requirements>
+		<requirement type="package" version="3.0f">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
diff -r 388f178f9e13 -r ebe280eca4a4 snpSift_annotate.xml
--- a/snpSift_annotate.xml	Thu Sep 13 22:33:33 2012 -0400
+++ b/snpSift_annotate.xml	Thu Sep 13 21:40:44 2012 -0500
@@ -5,6 +5,7 @@
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
+		<requirement type="package" version="3.0f">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
diff -r 388f178f9e13 -r ebe280eca4a4 snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Thu Sep 13 22:33:33 2012 -0400
+++ b/snpSift_caseControl.xml	Thu Sep 13 21:40:44 2012 -0500
@@ -5,6 +5,7 @@
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
+		<requirement type="package" version="3.0f">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
diff -r 388f178f9e13 -r ebe280eca4a4 snpSift_filter.xml
--- a/snpSift_filter.xml	Thu Sep 13 22:33:33 2012 -0400
+++ b/snpSift_filter.xml	Thu Sep 13 21:40:44 2012 -0500
@@ -7,6 +7,7 @@
 	java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
 	-->
 	<requirements>
+		<requirement type="package" version="3.0f">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
diff -r 388f178f9e13 -r ebe280eca4a4 snpSift_int.xml
--- a/snpSift_int.xml	Thu Sep 13 22:33:33 2012 -0400
+++ b/snpSift_int.xml	Thu Sep 13 21:40:44 2012 -0500
@@ -5,6 +5,7 @@
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
+		<requirement type="package" version="3.0f">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>