diff tool_dependencies.xml @ 50:857a85571395 draft

Uploaded

--- a/tool_dependencies.xml	Wed Sep 10 04:06:39 2014 -0400
+++ b/tool_dependencies.xml	Thu Sep 18 16:44:24 2014 -0400
@@ -60,8 +60,6 @@
     <package name="deepTools" version="1.5.9.1">
         <install version="1.0">
             <actions>
-                <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
-                <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
                     <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.7.7" />
@@ -79,12 +77,15 @@
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard 351890e3db9a443484c5c349791b7247163cc94f</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                <action type="setup_python_environment">
+                   <repository changeset_revision="74d009a2a4cb" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                       <package name="python" version="2.7" />
+                   </repository>
+                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
+                    <package>https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.9.1.tar.gz</package>
+
                 </action>
+
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                     <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>