Mercurial > repos > cmonjeau > package_stacks_1_18

diff tool_dependencies.xml @ 0:6bb02bb29819 draft default tip

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Imported from capsule None
author cmonjeau
date Mon, 24 Aug 2015 05:21:22 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 24 05:21:22 2015 -0400
@@ -0,0 +1,79 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="stacks" version="1.18">
+        <install version="1.0">
+            <actions>
+<!-- compile stacks -->
+                <action type="download_by_url">http://creskolab.uoregon.edu/stacks/source/stacks-1.18.tar.gz</action>
+		<action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+		<action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+
+		<!-- move binary into $INSTALL_dir -->
+		<!--action type="move_file">
+				     <source>ustacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>pstacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>estacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>cstacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>sstacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>hstacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>process_radtags</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>process_shortreads</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>kmer_filter</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>clone_filter</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>genotypes</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>populations</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action>
+		<action type="move_file">
+				     <source>phasedstacks</source>
+				     <destination>$INSTALL_DIR</destination>
+				</action-->
+
+		<!-- create env.sh -->
+                <action type="set_environment">
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
+                        <environment_variable name="INSTALL_DIR" action="set_to">$INSTALL_DIR/</environment_variable>
+                </action>
+ 
+           </actions>
+
+        </install>
+        <readme>
+            This package installs STACKS from the sources available
+        </readme>
+    </package>
+</tool_dependency>