diff mothur/tool_dependencies.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tool_dependencies.xml	Tue Dec 04 11:05:19 2012 -0600
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="mothur" version="1.27">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action>
+                <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
+                <action type="shell_command">cd Mothur.source &amp;&amp; make</action>
+                <action type="move_file">
+                    <source>Mothur.source/mothur</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>Mothur.source/uchime</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+These links provide information for building the Mothur package in most environments .
+
+http://www.mothur.org/wiki/Download_mothur
+
+http://www.mothur.org/wiki/Installation
+
+http://www.mothur.org/wiki/Makefile_options
+
+        </readme>
+    </package>
+    <!-- 
+      http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
+    -->
+</tool_dependency>
+