# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1353966866 21600
# Node ID 1cae7fb31da73a6e9cdd3dd7d56fae1f05756389
# Parent  244c09911d7a3d6924196778899fd28b7609ec17
SnpEffv3.1

diff -r 244c09911d7a -r 1cae7fb31da7 snpEff.xml
--- a/snpEff.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/snpEff.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -6,7 +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="3.0">snpEff</requirement>
+		<requirement type="package" version="3.1">snpEff</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>
diff -r 244c09911d7a -r 1cae7fb31da7 snpEff_download.xml
--- a/snpEff_download.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/snpEff_download.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -1,7 +1,7 @@
 <tool id="snpEff_download" name="SnpEff Download" version="1.0">
 	<description>Download a new database</description>
 	<requirements>
-		<requirement type="package" version="3.0">snpEff</requirement>
+		<requirement type="package" version="3.1">snpEff</requirement>
 	</requirements>
 	<command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 	<inputs>
diff -r 244c09911d7a -r 1cae7fb31da7 snpSift_annotate.xml
--- a/snpSift_annotate.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/snpSift_annotate.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -5,7 +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="1.7">SnpSift</requirement>
+                <requirement type="package" version="3.1">snpEff</requirement>
 	</requirements>
 	<command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
 	<inputs>
diff -r 244c09911d7a -r 1cae7fb31da7 snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/snpSift_caseControl.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -5,7 +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="1.7">SnpSift</requirement>
+                <requirement type="package" version="3.1">snpEff</requirement>
 	</requirements>
 	<command>
 		java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
diff -r 244c09911d7a -r 1cae7fb31da7 snpSift_filter.xml
--- a/snpSift_filter.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/snpSift_filter.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -7,7 +7,7 @@
 	java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
 	-->
 	<requirements>
-		<requirement type="package" version="1.7">SnpSift</requirement>
+                <requirement type="package" version="3.1">snpEff</requirement>
 	</requirements>
 	<command>
 		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
diff -r 244c09911d7a -r 1cae7fb31da7 snpSift_int.xml
--- a/snpSift_int.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/snpSift_int.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -5,7 +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="1.7">SnpSift</requirement>
+                <requirement type="package" version="3.1">snpEff</requirement>
 	</requirements>
 	<command>
 		cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
diff -r 244c09911d7a -r 1cae7fb31da7 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 21 18:52:07 2012 -0500
+++ b/tool_dependencies.xml	Mon Nov 26 15:54:26 2012 -0600
@@ -1,35 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snpEff" version="3.0">
+    <package name="snpEff" version="3.1">
         <install version="1.0">
             <actions>
-                <action type="shell_command">wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff/scripts</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-    <package name="SnpSift" version="1.7">
-        <install version="1.0">
-            <actions>
-                <action type="shell_command">mkdir SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar</action>
+                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip</action>
                 <action type="move_directory_files">
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/SnpSift</environment_variable>
+                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
                 </action>
             </actions>
         </install>