Mercurial > repos > jjohnson > snpeff_with_dep

changeset 17:aab5e0adb26d

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Remove environment requirement
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 18:23:28 -0500
parents 24c77a318a0f
children 4daa36729f67
files snpEff.xml snpEff_download.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml
diffstat 6 files changed, 0 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/snpEff.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpEff.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -7,7 +7,6 @@
 	-->
 	<requirements>
 		<requirement type="package" version="3.0">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>
 	<inputs>
--- a/snpEff_download.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpEff_download.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -2,7 +2,6 @@
 	<description>Download a new database</description>
 	<requirements>
 		<requirement type="package" version="3.0">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>
 	<inputs>
--- a/snpSift_annotate.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpSift_annotate.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -6,7 +6,6 @@
 	-->
 	<requirements>
 		<requirement type="package" version="1.7">SnpSift</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>
 	<inputs>
--- a/snpSift_caseControl.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpSift_caseControl.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -6,7 +6,6 @@
 	-->
 	<requirements>
 		<requirement type="package" version="1.7">SnpSift</requirement>
-		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
 		java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
--- a/snpSift_filter.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpSift_filter.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -8,7 +8,6 @@
 	-->
 	<requirements>
 		<requirement type="package" version="1.7">SnpSift</requirement>
-		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
 		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
--- a/snpSift_int.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpSift_int.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -6,7 +6,6 @@
 	-->
 	<requirements>
 		<requirement type="package" version="1.7">SnpSift</requirement>
-		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
 		cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output