diff tool_dependencies.xml @ 25:c361b3fb806e

added Nicola Path 2.0

--- a/tool_dependencies.xml	Mon May 19 20:00:44 2014 -0400
+++ b/tool_dependencies.xml	Tue Jun 03 17:31:28 2014 +1000
@@ -1,44 +1,28 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    
+    <package name="R" version="3.0.3">
+        <repository name="package_r_3_0_3" owner="iuc" />
+    </package>
+    
     <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
+        <repository name="package_samtools_0_1_18" owner="devteam" />
     </package>
 
-
    <package name="bedtools" version="2.17.0">
        <install version="1.0">
-           <actions>
-		<action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
-		<action type="shell_command">make all</action>
-		<action type="make_directory">$INSTALL_DIR/bin</action>
-		<action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>                                
-		<action type="set_environment">
-		   <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-		</action>
-           </actions>
+        <actions>
+            <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
+            <action type="shell_command">make all</action>
+            <action type="make_directory">$INSTALL_DIR/bin</action>
+            <action type="move_directory_files">
+                <source_directory>bin</source_directory>
+                <destination_directory>$INSTALL_DIR/bin</destination_directory>
+            </action>                   
+    		<action type="set_environment">
+    		   <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+    		</action>
+        </actions>
        </install>
        <readme>
 		GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required
@@ -48,13 +32,7 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action>
-                <action type="shell_command">rm -rf bedtools_installation_guide.txt</action>
-                <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action>
-                <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action>
-		<action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action>
-		<action type="make_directory">$INSTALL_DIR/bin</action>
-		<action type="make_directory">$INSTALL_DIR/bin/scripts</action>
-		<action type="move_file">
+                <action type="move_file">
                     <source>contra.py</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
@@ -62,7 +40,7 @@
                     <source>baseline.py</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
-		<action type="move_directory_files">
+                <action type="move_directory_files">
                     <source_directory>scripts</source_directory>
                     <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory>
                 </action>