Mercurial > repos > jjohnson > snpeff_with_dep

diff tool_dependencies.xml @ 20:1cae7fb31da7

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SnpEffv3.1
author Jim Johnson <jj@umn.edu>
date Mon, 26 Nov 2012 15:54:26 -0600
parents 244c09911d7a
children 077c84a53846
line wrap: on
line diff
--- 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>