Mercurial > repos > jjohnson > snpeff_with_dep

changeset 11:e9e4ff80e72b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Release version 3.0
author Jim Johnson <jj@umn.edu>
date Tue, 18 Sep 2012 09:28:08 -0500
parents 9cd24981dbd2
children 57c46f7fe70b
files snpEff.xml snpEff_download.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml tool_dependencies.xml
diffstat 7 files changed, 12 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/snpEff.xml	Tue Sep 18 08:36:28 2012 -0500
+++ b/snpEff.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -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="3.0f">snpEff</requirement>
+		<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>
--- a/snpEff_download.xml	Tue Sep 18 08:36:28 2012 -0500
+++ b/snpEff_download.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -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="3.0f">snpEff</requirement>
+		<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>
--- a/snpSift_annotate.xml	Tue Sep 18 08:36:28 2012 -0500
+++ b/snpSift_annotate.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -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="3.0f">snpEff</requirement>
+		<requirement type="package" version="3.0">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	Tue Sep 18 08:36:28 2012 -0500
+++ b/snpSift_caseControl.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -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="3.0f">snpEff</requirement>
+		<requirement type="package" version="3.0">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
--- a/snpSift_filter.xml	Tue Sep 18 08:36:28 2012 -0500
+++ b/snpSift_filter.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -7,7 +7,7 @@
 	java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
 	-->
 	<requirements>
-		<requirement type="package" version="3.0f">snpEff</requirement>
+		<requirement type="package" version="3.0">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
--- a/snpSift_int.xml	Tue Sep 18 08:36:28 2012 -0500
+++ b/snpSift_int.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -5,7 +5,7 @@
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-		<requirement type="package" version="3.0f">snpEff</requirement>
+		<requirement type="package" version="3.0">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>
--- a/tool_dependencies.xml	Tue Sep 18 08:36:28 2012 -0500
+++ b/tool_dependencies.xml	Tue Sep 18 09:28:08 2012 -0500
@@ -3,27 +3,16 @@
     <set_environment version="1.0">
         <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
     </set_environment>
-    <package name="snpEff" version="3.0f">
+    <package name="snpEff" version="3.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip</action>
-                <action type="shell_command">unzip snpEff_latest_core.zip</action>
-                <action type="move_file">
-                    <source>snpEff_3_0/SnpSift.jar</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
+                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip</action>
                 <action type="move_file">
-                    <source>snpEff_3_0/snpEff.jar</source>
-                    <destination>$INSTALL_DIR/bin</destination>
+                    <source>snpEff_v3_0_core.zip</source>
+                    <destination>$INSTALL_DIR</destination>
                 </action>
-                <action type="move_file">
-                    <source>snpEff_3_0/snpEff.config</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>snpEff_3_0/scripts</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
+                <action type="shell_command">unzip snpEff_v3_0_core.zip</action>
+                <action type="shell_command">ln -s snpEff_3_0 bin</action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>