diff tool_dependencies.xml @ 0:99a10425de93 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 15 03:17:15 2013 -0400
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="eigen3" version="3.1.3">
+        <repository changeset_revision="6a1c187f36aa" name="package_eigen_3_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="openbabel" version="2.3.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz</action>
+
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="6a1c187f36aa" name="package_eigen_3_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="eigen3" version="3.1.3" />
+                    </repository>
+                </action>
+
+                <!--
+                    Huge hack, to point to the actual python lib path. Cmake gets confused with mixed python versions (2.x and 3.x) and we need to point explicitely to the recent version.
+                -->
+                <action type="shell_command">cmake . -DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN3_INCLUDE_DIR=$EIGEN3_SOURCE_PATH -DPYTHON_LIBRARY=`python -c 'import distutils.sysconfig; print "%s/libpython%s.so" % (distutils.sysconfig.get_config_var("LIBPL"), distutils.sysconfig.get_python_version())'`</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</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</environment_variable>
+                    <!-- internal variables for open babel -->
+                    <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable>
+                    <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.3.2</environment_variable>
+                    <!-- galaxy variables for other tool wrappers -->
+                    <environment_variable action="set_to" name="OPENBABEL_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable action="set_to" name="OPENBABEL_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling OpenBabel requires g++ and CMake 2.4+. Optional but required for a few features are the cairo development libraries. OPENBABEL_INCLUDE_DIR and OPENBABEL_LIB_DIR can be accessed from other tool wrappers.</readme>
+    </package>
+</tool_dependency>