Mercurial > repos > jjohnson > snpeff_with_dep

diff tool_dependencies.xml @ 12:57c46f7fe70b

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tool_dependencies.xml changes
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 14:42:09 -0500
parents e9e4ff80e72b
children d57983929080
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Sep 18 09:28:08 2012 -0500
+++ b/tool_dependencies.xml	Fri Sep 21 14:42:09 2012 -0500
@@ -1,20 +1,19 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <set_environment version="1.0">
-        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
+        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/snpEff</environment_variable>
     </set_environment>
     <package name="snpEff" version="3.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip</action>
-                <action type="move_file">
-                    <source>snpEff_v3_0_core.zip</source>
-                    <destination>$INSTALL_DIR</destination>
+                <action type="shell_command">wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
-                <action type="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">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable>
                 </action>
             </actions>
         </install>