Mercurial > repos > bjoern-gruening > augustus

changeset 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 d5d5999ff4f1
children a4fab0c1ae1a
files augustus.xml readme.txt tool_dependencies.xml
diffstat 3 files changed, 40 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/augustus.xml	Thu Mar 15 10:09:28 2012 +0100
+++ b/augustus.xml	Tue Oct 30 06:29:50 2012 -0400
@@ -1,5 +1,8 @@
-<tool id="augustus" name="Augustus" version="0.1">
-	<description>gen prediction for eukaryotic genomes</description>
+<tool id="augustus" name="Augustus" version="0.2">
+	<description>gene prediction for eukaryotic genomes</description>
+    <requirements>
+        <requirement type="package" version="2.6.1">augustus</requirement>
+    </requirements>
     <command>augustus
         --strand=$strand
         $noInFrameStop
@@ -113,9 +116,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">augustus</requirement>
-    </requirements>
     <help>
 
 **What it does**
--- a/readme.txt	Thu Mar 15 10:09:28 2012 +0100
+++ b/readme.txt	Tue Oct 30 06:29:50 2012 -0400
@@ -53,6 +53,7 @@
 =======
 
 v0.1 - Initial public release
+v0.2 - Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
 
 
 Wrapper Licence (MIT/BSD style)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 30 06:29:50 2012 -0400
@@ -0,0 +1,34 @@
+<?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>