Mercurial > repos > jjohnson > augustus_dep

changeset 3:75675bc1aafb draft

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Upgrade to augustus version 2.6.1
author Jim Johnson <jj@umn.edu>
date Tue, 23 Oct 2012 09:05:09 -0500
parents d088c697396d
children 06b5da1079d8
files augustus.xml tool_dependencies.xml
diffstat 2 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/augustus.xml	Mon Oct 22 13:05:34 2012 -0500
+++ b/augustus.xml	Tue Oct 23 09:05:09 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="augustus" name="Augustus" version="0.2">
 	<description>gene prediction for eukaryotic genomes</description>
     <requirements>
-        <requirement type="package" version="2.5.5">augustus</requirement>
+        <requirement type="package" version="2.6.1">augustus</requirement>
     </requirements>
     <command>augustus
         --strand=$strand
--- a/tool_dependencies.xml	Mon Oct 22 13:05:34 2012 -0500
+++ b/tool_dependencies.xml	Tue Oct 23 09:05:09 2012 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="augustus" version="2.5.5">
+    <package name="augustus" version="2.6.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz</action>
+                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
                 <action type="shell_command">make</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>
@@ -18,6 +18,9 @@
                     <destination_directory>$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">