diff tool_dependencies.xml @ 3:0c42bebab126 draft default tip

Uploaded

--- a/tool_dependencies.xml	Thu Feb 07 16:57:42 2013 -0500
+++ b/tool_dependencies.xml	Thu Feb 07 16:58:40 2013 -0500
@@ -1,47 +1,20 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
+    <package name="obo_scripts" version="1.0.1">
         <install version="1.0">
             <actions>
-                <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
-                <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
-                <action type="shell_command">git submodule update --recursive</action>
-                <action type="shell_command">make</action>
+                <action type="shell_command">git clone http://github.com/cmungall/obo-scripts</action>
                 <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
                 <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
-FreeBayes requires g++ and the standard C and C++ development libraries.
-Additionally, cmake is required for building the BamTools API.
-        </readme>
-    </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.
+		obo_scripts require perl to be installed.
         </readme>
     </package>
 </tool_dependency>