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diff tool_dependencies.xml @ 4:796814f16b12

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Add tool_dependencies.xml and update to new augustus version. Thanks to James Johnson for the patch.
author bjoern-gruening
date Tue, 30 Oct 2012 06:29:50 -0400
parents
children a4fab0c1ae1a
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 30 06:29:50 2012 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="augustus" version="2.6.1">
+        <install version="1.0">
+            <actions>
+                <!-- the first command puts us in the dir for the package name: "augustus"-->
+                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>scripts</source_directory>
+                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>config</source_directory>
+                    <destination_directory>$INSTALL_DIR/config</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>http://augustus.gobics.de/binaries/README.TXT</readme>
+    </package>
+</tool_dependency>