diff tool_dependencies.xml @ 5:a4fab0c1ae1a

Uploaded

--- a/tool_dependencies.xml	Tue Oct 30 06:29:50 2012 -0400
+++ b/tool_dependencies.xml	Sun Jun 09 07:54:25 2013 -0400
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="augustus" version="2.6.1">
+    <set_environment version="1.0">
+        <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="augustus" version="2.7">
         <install version="1.0">
             <actions>
-                <!-- the first command puts us in the dir for the package name: "augustus"-->
-                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
+                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz</action>
                 <action type="shell_command">make</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>
@@ -20,15 +22,15 @@
                 </action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$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>
+        <readme>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
+It can be used as an ab initio program, which means it bases its prediction purely on the
+sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
+such as EST, MS/MS, protein alignments and synthenic genomic alignments.
+http://augustus.gobics.de/binaries/README.TXT</readme>
     </package>
 </tool_dependency>