Mercurial > repos > jjohnson > snpeff_with_dep

changeset 1:ebe280eca4a4

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Add package requirement
author Jim Johnson <jj@umn.edu>
date Thu, 13 Sep 2012 21:40:44 -0500
parents 388f178f9e13
children 5248f48fa4ee
files snpEff.xml snpEff_download.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml
diffstat 6 files changed, 6 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>