Mercurial > repos > bonsai > sortmerna

diff tool_dependencies.xml @ 0:2e7f0da431e3 draft default tip

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Uploaded version 1.0
author bonsai
date Tue, 30 Apr 2013 13:12:35 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 30 13:12:35 2013 -0400
@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="sortmerna" version="1.7">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-1.7.tar.gz</action>
+                <action type="shell_command">./configure</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make check</action>
+                <action type="move_file">
+                    <source>sortmerna</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>buildtrie</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>scripts/merge-paired-reads.sh</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>rRNA_databases</source_directory>
+                    <destination_directory>$INSTALL_DIR/rRNA_databases</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>automata</source_directory>
+                    <destination_directory>$INSTALL_DIR/automata</destination_directory>
+                </action>
+                <action type="set_environment">
+		    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <action type="set_environment">
+		    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed.
+	</readme>
+    </package>
+</tool_dependency>