# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1379519396 18000
# Node ID 937367efb1da94adf2c43def2e6285699e5ed948
# Parent  13b6ad2ddace6ad4e50ca24f2df725736aa60c72
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.

diff -r 13b6ad2ddace -r 937367efb1da snpEff.xml
--- a/snpEff.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpEff.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -64,11 +64,11 @@
 		<requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
+SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
-then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
+then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download  -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ;
 fi";
-java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 
+java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 
 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
   -spliceSiteSize $spliceSiteSize
 #end if
diff -r 13b6ad2ddace -r 937367efb1da snpEff_download.xml
--- a/snpEff_download.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpEff_download.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -3,7 +3,7 @@
 	<requirements>
 		<requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
-	<command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+	<command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 	<inputs>
 		<param name="genomeVersion" type="select" label="Genome">
 			<options from_file="snpeffect_genomedb.loc">
diff -r 13b6ad2ddace -r 937367efb1da snpSift_annotate.xml
--- a/snpSift_annotate.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpSift_annotate.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -8,7 +8,7 @@
                 <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-        java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd 
+        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
         #if $annotate.id :
           -id
         #elif $annotate.info_ids.__str__.strip() != '' :
diff -r 13b6ad2ddace -r 937367efb1da snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpSift_caseControl.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -8,7 +8,7 @@
                 <requirement type="package" version="3.2">snpEff</requirement>
   </requirements>
   <command>
-    java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q 
+    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
     #if $name.__str__.strip() != '':
       -name $name
     #end if
diff -r 13b6ad2ddace -r 937367efb1da snpSift_filter.xml
--- a/snpSift_filter.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpSift_filter.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -5,7 +5,7 @@
                 <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
+		java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
                 #if $filterId and len($filterId.__str__.strip()) > 0:
 			--filterId = "$filterId"
                 #end if
diff -r 13b6ad2ddace -r 937367efb1da snpSift_int.xml
--- a/snpSift_int.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpSift_int.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -8,7 +8,7 @@
                 <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-		java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+		java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
diff -r 13b6ad2ddace -r 937367efb1da tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 13 12:45:07 2013 -0500
+++ b/tool_dependencies.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="snpEff" version="3.2">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="snpeff_3_2" owner="jjohnson" changeset_revision="8ece49cfe180" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_snpeff_3_2" owner="jjohnson" changeset_revision="8081a3ff0d87" />
     </package>
 </tool_dependency>