diff tool_dependencies.xml @ 18:cff63cf0dea8

Update tool_dependencies to install package from pip

--- a/tool_dependencies.xml	Mon Aug 31 11:41:48 2015 +0100
+++ b/tool_dependencies.xml	Mon Aug 31 14:13:03 2015 +0100
@@ -1,13 +1,29 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="50b86df1f968" name="package_matplotlib_1_2"
-            owner="iuc" prior_installation_required="True"
-            />
+    <package name="ez_setup" version="0.9">
+        <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc"
+            prior_installation_required="True"/>
     </package>
-    <package name="pysam" version="0.8.3">
-        <repository changeset_revision="ee642ed79a3b" name="package_python_2_7_pysam_0_8_3"
-            owner="iuc" prior_installation_required="True"
-            />
+    <package name="riboplot" version="0.1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://pypi.python.org/packages/source/r/riboplot/riboplot-0.1.0.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc">
+                        <package name="ez_setup" version="0.9" />
+                    </repository>
+                </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 $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+           Requires installation of matplotlib 1.3.1 and pysam 0.8.3. RNA coverage requires bedtools installed.
+        </readme>
     </package>
 </tool_dependency>