Mercurial > repos > devteam > snpeff_with_dep

diff snpeff_with_dep-244c09911d7a/tool_dependencies.xml @ 0:d8bd4326dc3a draft

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author devteam
date Thu, 27 Sep 2012 13:40:17 -0400
parents
children 515163fbe70f
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpeff_with_dep-244c09911d7a/tool_dependencies.xml	Thu Sep 27 13:40:17 2012 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snpEff" version="3.0">
+        <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">$INSTALL_DIR/snpEff/scripts</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+    <package name="SnpSift" version="1.7">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">mkdir SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/SnpSift</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>
+